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Retrotransposition facilitated the establishment of a primary plastid in the thecate amoeba Paulinella. Proc Natl Acad Sci U S A 2022; 119:e2121241119. [PMID: 35639693 DOI: 10.1073/pnas.2121241119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
SignificancePrimary endosymbiosis allowed the evolution of complex life on Earth. In this process, a prokaryote was engulfed and retained in the cytoplasm of another microbe, where it developed into a new organelle (mitochondria and plastids). During organelle evolution, genes from the endosymbiont are transferred to the host nuclear genome, where they must become active despite differences in the genetic nature of the "partner" organisms. Here, we show that in the amoeba Paulinella micropora, which harbors a nascent photosynthetic organelle, the "copy-paste" mechanism of retrotransposition allowed domestication of endosymbiont-derived genes in the host nuclear genome. This duplication mechanism is widespread in eukaryotes and may be a major facilitator for host-endosymbiont integration and the evolution of organelles.
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Jia A, Zheng Y, Chen H, Wang Q. Regulation and Functional Complexity of the Chlorophyll-Binding Protein IsiA. Front Microbiol 2021; 12:774107. [PMID: 34867913 PMCID: PMC8635728 DOI: 10.3389/fmicb.2021.774107] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 10/25/2021] [Indexed: 11/17/2022] Open
Abstract
As the oldest known lineage of oxygen-releasing photosynthetic organisms, cyanobacteria play the key roles in helping shaping the ecology of Earth. Iron is an ideal transition metal for redox reactions in biological systems. Cyanobacteria frequently encounter iron deficiency due to the environmental oxidation of ferrous ions to ferric ions, which are highly insoluble at physiological pH. A series of responses, including architectural changes to the photosynthetic membranes, allow cyanobacteria to withstand this condition and maintain photosynthesis. Iron-stress-induced protein A (IsiA) is homologous to the cyanobacterial chlorophyll (Chl)-binding protein, photosystem II core antenna protein CP43. IsiA is the major Chl-containing protein in iron-starved cyanobacteria, binding up to 50% of the Chl in these cells, and this Chl can be released from IsiA for the reconstruction of photosystems during the recovery from iron limitation. The pigment–protein complex (CPVI-4) encoded by isiA was identified and found to be expressed under iron-deficient conditions nearly 30years ago. However, its precise function is unknown, partially due to its complex regulation; isiA expression is induced by various types of stresses and abnormal physiological states besides iron deficiency. Furthermore, IsiA forms a range of complexes that perform different functions. In this article, we describe progress in understanding the regulation and functions of IsiA based on laboratory research using model cyanobacteria.
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Affiliation(s)
- Anqi Jia
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Yanli Zheng
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Hui Chen
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Qiang Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
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Qiao Y, Wang W, Lu X. High Light Induced Alka(e)ne Biodegradation for Lipid and Redox Homeostasis in Cyanobacteria. Front Microbiol 2020; 11:1659. [PMID: 32765469 PMCID: PMC7379126 DOI: 10.3389/fmicb.2020.01659] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/25/2020] [Indexed: 01/09/2023] Open
Abstract
Cyanobacteria are the oldest photosynthetic microorganisms with good environmental adaptability. They are ubiquitous in light-exposed habitats on Earth. In recent years, cyanobacteria have become an ideal platform for producing biofuels and biochemicals from solar energy and carbon dioxide. Alka(e)nes are the main constituents of gasoline, diesel, and jet fuels. Alka(e)ne biosynthesis pathways are present in all sequenced cyanobacteria. Most cyanobacteria biosynthesize long chain alka(e)nes via acyl-acyl-carrier proteins reductase (AAR) and aldehyde-deformylating oxygenase (ADO). Alka(e)nes can be biodegraded by a variety of cyanobacteria, which lack a β-oxidation pathway. However, the mechanisms of alka(e)ne biodegradation in cyanobacteria remain elusive. In this study, a cyanobacterial alka(e)ne biodegradation pathway was uncovered by in vitro enzyme assays. Under high light, alka(e)nes in the membrane can be converted into alcohols and aldehydes by ADO, and aldehyde dehydrogenase (ALDH) can then convert the aldehydes into fatty acids to maintain lipid homeostasis in cyanobacteria. As highly reduced molecules, alka(e)nes could serve as electron donors to further reduce partially reduced reactive oxygen species (ROS) in cyanobacteria under high light. Alka(e)ne biodegradation may serve as an emergency mechanism for responding to the oxidative stress generated by excess light exposure. This study will shed new light on the roles of alka(e)ne metabolism in cyanobacteria. It is important to reduce the content of ROS by optimization of cultivation and genetic engineering for efficient alka(e)ne biosynthesis in cyanobacteria.
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Affiliation(s)
- Yue Qiao
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Weihua Wang
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Xuefeng Lu
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,Dalian National Laboratory for Clean Energy, Dalian, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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4
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Response of Synechocystis sp. PCC 6803 to UV radiations by alteration of polyamines associated with thylakoid membrane proteins. World J Microbiol Biotechnol 2018; 35:8. [PMID: 30569232 DOI: 10.1007/s11274-018-2580-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Accepted: 12/11/2018] [Indexed: 11/27/2022]
Abstract
The responses of Synechocystis sp. PCC 6803 exposed to UVA, UVB and UVC for at least 3 h were investigated with the emphasis on the changes of polyamines (PAs) levels in whole cells, thylakoid membrane fraction, and thylakoid membrane-associated proteins fraction. All UV radiations caused a slight decrease on cell growth but a drastic reduction of photosynthetic efficiency of Synechocystis cells. UV radiations, especially UVB and UVC, severely decreased the levels of PAs associated with thylakoid membrane proteins. The decreased PAs levels as affected by UV radiation correlated well with the decrease of photosynthetic efficiency, suggesting the role of PAs for the maintenance of photosynthetic activity of Synechocystis. PAs, especially spermidine (Spd) and putrescine (Put), were found abundantly in the thylakoid membrane fraction, and these PAs were associated mainly with the PSI trimer complex. Importantly, the exposure of Synechocystis cells to all UV radiations for 3 h resulted in the increase of Spd associated with the PSII monomer and dimer complex, suggesting its protective role against UV radiations despite the overall decrease of PAs.
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Lee J, Yang EC, Graf L, Yang JH, Qiu H, Zelzion U, Chan CX, Stephens TG, Weber APM, Boo GH, Boo SM, Kim KM, Shin Y, Jung M, Lee SJ, Yim HS, Lee JH, Bhattacharya D, Yoon HS. Analysis of the Draft Genome of the Red Seaweed Gracilariopsis chorda Provides Insights into Genome Size Evolution in Rhodophyta. Mol Biol Evol 2018; 35:1869-1886. [DOI: 10.1093/molbev/msy081] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- JunMo Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Eun Chan Yang
- Marine Ecosystem Research Center, Korea Institute of Ocean Science and Technology, Busan, Korea
| | - Louis Graf
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Ji Hyun Yang
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Huan Qiu
- Department of Ecology Evolution and Natural Resources, Rutgers University, New Brunswick, NJ
| | - Udi Zelzion
- Department of Ecology Evolution and Natural Resources, Rutgers University, New Brunswick, NJ
| | - Cheong Xin Chan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Timothy G Stephens
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Andreas P M Weber
- Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-University, Duesseldorf, Germany
| | - Ga Hun Boo
- Department of Biology, Chungnam National University, Daejeon, Korea
| | - Sung Min Boo
- Department of Biology, Chungnam National University, Daejeon, Korea
| | - Kyeong Mi Kim
- National Marine Biodiversity Institute of Korea, Seocheon, Korea
| | - Younhee Shin
- Bioinformatics Group, R&D Center, Insilicogen, Inc., Suwon, Korea
| | - Myunghee Jung
- Bioinformatics Group, R&D Center, Insilicogen, Inc., Suwon, Korea
| | | | - Hyung-Soon Yim
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, Korea
| | - Jung-Hyun Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, Korea
| | | | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
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Zhu Y, Pei G, Niu X, Shi M, Zhang M, Chen L, Zhang W. Metabolomic analysis reveals functional overlapping of three signal transduction proteins in regulating ethanol tolerance in cyanobacterium Synechocystis sp. PCC 6803. MOLECULAR BIOSYSTEMS 2014; 11:770-82. [PMID: 25502571 DOI: 10.1039/c4mb00651h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Low ethanol tolerance is a crucial factor that restricts the feasibility of bioethanol production in renewable cyanobacterial systems. Our previous studies showed that several transcriptional regulators were differentially regulated by exogenous ethanol in Synechocystis. In this study, by constructing knockout mutants of 34 Synechocystis putative transcriptional regulator-encoding genes and analyzing their phenotypes under ethanol stress, we found that three mutants of regulatory gene sll1392, sll1712 and slr1860 grew poorly in the BG11 medium supplemented with ethanol when compared with the wild type in the same medium, suggesting that the genes may be involved in the regulation of ethanol tolerance. To decipher the regulatory mechanism, targeted LC-MS and untargeted GC-MS approaches were employed to determine metabolic profiles of the three mutants and the wild type under both normal and ethanol stress conditions. The results were then subjected to PCA and WGCNA analyses to determine the responsive metabolites and metabolic modules related to ethanol tolerance. Interestingly, the results showed that there was a significant overlapping of the responsive metabolites and metabolic modules between three regulatory proteins, suggesting that a possible crosstalk between various regulatory proteins may be involved in combating against ethanol toxicity in Synechocystis. The study provided new insights into ethanol-tolerance regulation and knowledge important to rational tolerance engineering in Synechocystis.
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Affiliation(s)
- Ye Zhu
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, P. R. China.
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Cheng D, He Q. PfsR is a key regulator of iron homeostasis in Synechocystis PCC 6803. PLoS One 2014; 9:e101743. [PMID: 25010795 PMCID: PMC4092027 DOI: 10.1371/journal.pone.0101743] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 06/10/2014] [Indexed: 02/04/2023] Open
Abstract
Iron is an essential cofactor in numerous cellular processes. The iron deficiency in the oceans affects the primary productivity of phytoplankton including cyanobacteria. In this study, we examined the function of PfsR, a TetR family transcriptional regulator, in iron homeostasis of the cyanobacterium Synechocystis PCC 6803. Compared with the wild type, the pfsR deletion mutant displayed stronger tolerance to iron limitation and accumulated significantly more chlorophyll a, carotenoid, and phycocyanin under iron-limiting conditions. The mutant also maintained more photosystem I and photosystem II complexes than the wild type after iron deprivation. In addition, the activities of photosystem I and photosystem II were much higher in pfsR deletion mutant than in wild-type cells under iron-limiting conditions. The transcripts of pfsR were enhanced by iron limitation and inactivation of the gene affected pronouncedly expression of fut genes (encoding a ferric iron transporter), feoB (encoding a ferrous iron transporter), bfr genes (encoding bacterioferritins), ho genes (encoding heme oxygenases), isiA (encoding a chlorophyll-binding protein), and furA (encoding a ferric uptake regulator). The iron quota in pfsR deletion mutant cells was higher than in wild-type cells both before and after exposure to iron limitation. Electrophoretic mobility shift assays showed that PfsR bound to its own promoter and thereby auto-regulated its own expression. These data suggest that PfsR is a critical regulator of iron homeostasis.
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Affiliation(s)
- Dan Cheng
- Department of Applied Science, University of Arkansas at Little Rock, Little Rock, Arkansas, United States of America
| | - Qingfang He
- Department of Applied Science, University of Arkansas at Little Rock, Little Rock, Arkansas, United States of America
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Chen L, Zhu Y, Song Z, Wang J, Zhang W. An orphan response regulator Sll0649 involved in cadmium tolerance and metal homeostasis in photosynthetic Synechocystis sp. PCC 6803. J Proteomics 2014; 103:87-102. [DOI: 10.1016/j.jprot.2014.03.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 03/07/2014] [Accepted: 03/23/2014] [Indexed: 10/25/2022]
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Sánchez-Riego AM, López-Maury L, Florencio FJ. Glutaredoxins are essential for stress adaptation in the cyanobacterium Synechocystis sp. PCC 6803. FRONTIERS IN PLANT SCIENCE 2013; 4:428. [PMID: 24204369 PMCID: PMC3816324 DOI: 10.3389/fpls.2013.00428] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 10/10/2013] [Indexed: 05/10/2023]
Abstract
Glutaredoxins are small redox proteins able to reduce disulfides and mixed disulfides between GSH and proteins. Synechocystis sp. PCC 6803 contains three genes coding for glutaredoxins: ssr2061 (grxA) and slr1562 (grxB) code for dithiolic glutaredoxins while slr1846 (grxC) codes for a monothiolic glutaredoxin. We have analyzed the expression of these glutaredoxins in response to different stresses, such as high light, H2O2 and heat shock. Analysis of the mRNA levels showed that grxA is only induced by heat while grxC is repressed by heat shock and is induced by high light and H2O2. In contrast, grxB expression was maintained almost constant under all conditions. Analysis of GrxA and GrxC protein levels by western blot showed that GrxA increases in response to high light, heat or H2O2 while GrxC is only induced by high light and H2O2, in accordance with its mRNA levels. In addition, we have also generated mutants that have interrupted one, two, or three glutaredoxin genes. These mutants were viable and did not show any different phenotype from the WT under standard growth conditions. Nevertheless, analysis of these mutants under several stress conditions revealed that single grxA mutants grow slower after H2O2, heat and high light treatments, while mutants in grxB are indistinguishable from WT. grxC mutants were hypersensitive to treatments with H2O2, heat, high light and metals. A double grxAgrxC mutant was found to be even more sensitive to H2O2 than each corresponding single mutants. Surprisingly a mutation in grxB suppressed totally or partially the phenotypes of grxA and grxC mutants except the H2O2 sensitivity of the grxC mutant. This suggests that grxA and grxC participate in independent pathways while grxA and grxB participate in a common pathway for H2O2 resistance. The data presented here show that glutaredoxins are essential for stress adaptation in cyanobacteria, although their targets and mechanism of action remain unidentified.
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Affiliation(s)
| | | | - Francisco J. Florencio
- *Correspondence: Francisco J. Florencio, Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-CSIC, Av Americo Vespucio 49, E 41092 Seville, Spain e-mail:
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10
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Wang J, Chen L, Huang S, Liu J, Ren X, Tian X, Qiao J, Zhang W. RNA-seq based identification and mutant validation of gene targets related to ethanol resistance in cyanobacterial Synechocystis sp. PCC 6803. BIOTECHNOLOGY FOR BIOFUELS 2012; 5:89. [PMID: 23259593 PMCID: PMC3564720 DOI: 10.1186/1754-6834-5-89] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 12/04/2012] [Indexed: 05/03/2023]
Abstract
BACKGROUND Fermentation production of biofuel ethanol consumes agricultural crops, which will compete directly with the food supply. As an alternative, photosynthetic cyanobacteria have been proposed as microbial factories to produce ethanol directly from solar energy and CO2. However, the ethanol productivity from photoautotrophic cyanobacteria is still very low, mostly due to the low tolerance of cyanobacterial systems to ethanol stress. RESULTS To build a foundation necessary to engineer robust ethanol-producing cyanobacterial hosts, in this study we applied a quantitative transcriptomics approach with a next-generation sequencing technology, combined with quantitative reverse-transcript PCR (RT-PCR) analysis, to reveal the global metabolic responses to ethanol in model cyanobacterial Synechocystis sp. PCC 6803. The results showed that ethanol exposure induced genes involved in common stress responses, transporting and cell envelope modification. In addition, the cells can also utilize enhanced polyhydroxyalkanoates (PHA) accumulation and glyoxalase detoxication pathway as means against ethanol stress. The up-regulation of photosynthesis by ethanol was also further confirmed at transcriptional level. Finally, we used gene knockout strains to validate the potential target genes related to ethanol tolerance. CONCLUSION RNA-Seq based global transcriptomic analysis provided a comprehensive view of cellular response to ethanol exposure. The analysis provided a list of gene targets for engineering ethanol tolerance in cyanobacterium Synechocystis.
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Affiliation(s)
- Jiangxin Wang
- School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin, 300072, People's Republic of China
| | - Lei Chen
- School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin, 300072, People's Republic of China
| | - Siqiang Huang
- School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin, 300072, People's Republic of China
| | - Jie Liu
- School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin, 300072, People's Republic of China
| | - Xiaoyue Ren
- School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin, 300072, People's Republic of China
| | - Xiaoxu Tian
- School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin, 300072, People's Republic of China
| | - Jianjun Qiao
- School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin, 300072, People's Republic of China
| | - Weiwen Zhang
- School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin, 300072, People's Republic of China
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Majeed W, Zhang Y, Xue Y, Ranade S, Blue RN, Wang Q, He Q. RpaA regulates the accumulation of monomeric photosystem I and PsbA under high light conditions in Synechocystis sp. PCC 6803. PLoS One 2012; 7:e45139. [PMID: 23024802 PMCID: PMC3443226 DOI: 10.1371/journal.pone.0045139] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 08/13/2012] [Indexed: 11/22/2022] Open
Abstract
The response regulator RpaA was examined by targeted mutagenesis under high light conditions in Synechocystis sp. PCC 6803. A significant reduction in chlorophyll fluorescence from photosystem I at 77 K was observed in the RpaA mutant cells under high light conditions. Interestingly, the chlorophyll fluorescence emission from the photosystem I trimers at 77 K are similar to that of the wild type, while the chlorophyll fluorescence from the photosystem I monomers was at a much lower level in the mutant than in the wild type under high light conditions. The RpaA inactivation resulted in a dramatic reduction in the monomeric photosystem I and the D1 protein but not the CP47 content. However, there is no significant difference in the transcript levels of psaA or psbA or other genes examined, most of which are involved in photosynthesis, pigment biosynthesis, or stress responses. Under high light conditions, the growth of the mutant was affected, and both the chlorophyll content and the whole-chain oxygen evolution capability of the mutant were found to be significantly lower than those of the wild type, respectively. We propose that RpaA regulates the accumulation of the monomeric photosystem I and the D1 protein under high light conditions. This is the first report demonstrating that inactivation of a stress response regulator has specifically reduced the monomeric photosystem I. It suggests that PS I monomers and PS I trimers can be regulated independently for acclimation of cells to high light stress.
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Affiliation(s)
- Waqar Majeed
- Department of Applied Science, University of Arkansas at Little Rock, Little Rock, Arkansas, United States of America
| | - Yan Zhang
- High Tech Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong Province, China
| | - Yong Xue
- Department of Applied Science, University of Arkansas at Little Rock, Little Rock, Arkansas, United States of America
| | - Saurabh Ranade
- Department of Applied Science, University of Arkansas at Little Rock, Little Rock, Arkansas, United States of America
| | - Ryan Nastashia Blue
- Department of Applied Science, University of Arkansas at Little Rock, Little Rock, Arkansas, United States of America
| | - Qiang Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| | - Qingfang He
- Department of Applied Science, University of Arkansas at Little Rock, Little Rock, Arkansas, United States of America
- High Tech Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong Province, China
- * E-mail:
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Singh AK, Elvitigala T, Cameron JC, Ghosh BK, Bhattacharyya-Pakrasi M, Pakrasi HB. Integrative analysis of large scale expression profiles reveals core transcriptional response and coordination between multiple cellular processes in a cyanobacterium. BMC SYSTEMS BIOLOGY 2010; 4:105. [PMID: 20678200 PMCID: PMC2924297 DOI: 10.1186/1752-0509-4-105] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Accepted: 08/02/2010] [Indexed: 12/30/2022]
Abstract
BACKGROUND Cyanobacteria are the only known prokaryotes capable of oxygenic photosynthesis. They play significant roles in global biogeochemical cycles and carbon sequestration, and have recently been recognized as potential vehicles for production of renewable biofuels. Synechocystis sp. PCC 6803 has been extensively used as a model organism for cyanobacterial studies. DNA microarray studies in Synechocystis have shown varying degrees of transcriptome reprogramming under altered environmental conditions. However, it is not clear from published work how transcriptome reprogramming affects pre-existing networks of fine-tuned cellular processes. RESULTS We have integrated 163 transcriptome data sets generated in response to numerous environmental and genetic perturbations in Synechocystis. Our analyses show that a large number of genes, defined as the core transcriptional response (CTR), are commonly regulated under most perturbations. The CTR contains nearly 12% of Synechocystis genes found on its chromosome. The majority of genes in the CTR are involved in photosynthesis, translation, energy metabolism and stress protection. Our results indicate that a large number of differentially regulated genes identified in most reported studies in Synechocystis under different perturbations are associated with the general stress response. We also find that a majority of genes in the CTR are coregulated with 25 regulatory genes. Some of these regulatory genes have been implicated in cellular responses to oxidative stress, suggesting that reactive oxygen species are involved in the regulation of the CTR. A Bayesian network, based on the regulation of various KEGG pathways determined from the expression patterns of their associated genes, has revealed new insights into the coordination between different cellular processes. CONCLUSION We provide here the first integrative analysis of transcriptome data sets generated in a cyanobacterium. This compilation of data sets is a valuable resource to researchers for all cyanobacterial gene expression related queries. Importantly, our analysis provides a global description of transcriptional reprogramming under different perturbations and a basic framework to understand the strategies of cellular adaptations in Synechocystis.
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Affiliation(s)
- Abhay K Singh
- Department of Biology, Washington University, St Louis, MO 63130, USA
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Singh AK, Bhattacharyya-Pakrasi M, Elvitigala T, Ghosh B, Aurora R, Pakrasi HB. A systems-level analysis of the effects of light quality on the metabolism of a cyanobacterium. PLANT PHYSIOLOGY 2009; 151:1596-608. [PMID: 19759342 PMCID: PMC2773086 DOI: 10.1104/pp.109.144824] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Photosynthetic organisms experience changes in light quantity and light quality in their natural habitat. In response to changes in light quality, these organisms redistribute excitation energy and adjust photosystem stoichiometry to maximize the utilization of available light energy. However, the response of other cellular processes to changes in light quality is mostly unknown. Here, we report a systematic investigation into the adaptation of cellular processes in Synechocystis species PCC 6803 to light that preferentially excites either photosystem II or photosystem I. We find that preferential excitation of photosystem II and photosystem I induces massive reprogramming of the Synechocystis transcriptome. The rewiring of cellular processes begins as soon as Synechocystis senses the imbalance in the excitation of reaction centers. We find that Synechocystis utilizes the cyclic photosynthetic electron transport chain for ATP generation and a major part of the respiratory pathway to generate reducing equivalents and carbon skeletons during preferential excitation of photosystem I. In contrast, cytochrome c oxidase and photosystem I act as terminal components of the photosynthetic electron transport chain to produce sufficient ATP and limited amounts of NADPH and reduced ferredoxin during preferential excitation of photosystem II. To overcome the shortage of NADPH and reduced ferredoxin, Synechocystis preferentially activates transporters and acquisition pathways to assimilate ammonia, urea, and arginine over nitrate as a nitrogen source. This study provides a systematic analysis of cellular processes in cyanobacteria in response to preferential excitation and shows that the cyanobacterial cell undergoes significant adjustment of cellular processes, many of which were previously unknown.
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Long JC, Merchant SS. Photo-oxidative Stress Impacts the Expression of Genes Encoding Iron Metabolism Components in Chlamydomonas†. Photochem Photobiol 2008; 84:1395-403. [DOI: 10.1111/j.1751-1097.2008.00451.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Singh AK, Elvitigala T, Bhattacharyya-Pakrasi M, Aurora R, Ghosh B, Pakrasi HB. Integration of carbon and nitrogen metabolism with energy production is crucial to light acclimation in the cyanobacterium Synechocystis. PLANT PHYSIOLOGY 2008; 148:467-78. [PMID: 18599646 PMCID: PMC2528105 DOI: 10.1104/pp.108.123489] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Light drives the production of chemical energy and reducing equivalents in photosynthetic organisms required for the assimilation of essential nutrients. This process also generates strong oxidants and reductants that can be damaging to the cellular processes, especially during absorption of excess excitation energy. Cyanobacteria, like other oxygenic photosynthetic organisms, respond to increases in the excitation energy, such as during exposure of cells to high light (HL) by the reduction of antenna size and photosystem content. However, the mechanism of how Synechocystis sp. PCC 6803, a cyanobacterium, maintains redox homeostasis and coordinates various metabolic processes under HL stress remains poorly understood. In this study, we have utilized time series transcriptome data to elucidate the global responses of Synechocystis to HL. Identification of differentially regulated genes involved in the regulation, protection, and maintenance of redox homeostasis has offered important insights into the optimized response of Synechocystis to HL. Our results indicate a comprehensive integrated homeostatic interaction between energy production (photosynthesis) and energy consumption (assimilation of carbon and nitrogen). In addition, measurements of physiological parameters under different growth conditions showed that integration between the two processes is not a consequence of limitations in the external carbon and nitrogen levels available to the cells. We have also discovered the existence of a novel glycosylation pathway, to date known as an important nutrient sensor only in eukaryotes. Up-regulation of a gene encoding the rate-limiting enzyme in the hexosamine pathway suggests a regulatory role for protein glycosylation in Synechocystis under HL.
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Affiliation(s)
- Abhay K Singh
- Department of Biology , Washington University, St. Louis, Missouri 63130, USA
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Wang Q, Jantaro S, Lu B, Majeed W, Bailey M, He Q. The high light-inducible polypeptides stabilize trimeric photosystem I complex under high light conditions in Synechocystis PCC 6803. PLANT PHYSIOLOGY 2008; 147:1239-50. [PMID: 18502976 PMCID: PMC2442545 DOI: 10.1104/pp.108.121087] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2008] [Accepted: 05/19/2008] [Indexed: 05/21/2023]
Abstract
The high light-inducible polypeptides (HLIPs) are critical for survival under high light (HL) conditions in Synechocystis PCC 6803. In this article, we determined the localization of all four HLIPs in thylakoid protein complexes and examined effects of hli gene deletion on the photosynthetic protein complexes. The HliA and HliB proteins were found to be associated with trimeric photosystem I (PSI) complexes and the Slr1128 protein, whereas HliC was associated with PsaL and TMP14. The HliD was associated with partially dissociated PSI complexes. The PSI activities of the hli mutants were 3- to 4-fold lower than that of the wild type. The hli single mutants lost more than 30% of the PSI trimers after they were incubated in intermediate HL for 12 h. The reduction of PSI trimers were further augmented in these cells by the increase of light intensity. The quadruple hli deletion mutant contained less than one-half of PSI trimers following 12-h incubation in intermediate HL. It lost essentially all of the PSI trimers upon exposure to HL for 12 h. Furthermore, a mutant lacking both PSI trimers and Slr1128 showed growth defects similar to that of the quadruple hli deletion mutant under different light conditions. These results suggest that the HLIPs stabilize PSI trimers, interact with Slr1128, and protect cells under HL conditions.
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Affiliation(s)
- Qiang Wang
- Department of Applied Science, University of Arkansas, Little Rock, Arkansas 72204, USA
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Kilian O, Steunou AS, Grossman AR, Bhaya D. A novel two domain-fusion protein in cyanobacteria with similarity to the CAB/ELIP/HLIP superfamily: evolutionary implications and regulation. MOLECULAR PLANT 2008; 1:155-166. [PMID: 20031922 DOI: 10.1093/mp/ssm019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Vascular plants contain abundant, light-harvesting complexes in the thylakoid membrane that are non-covalently associated with chlorophylls and carotenoids. These light-harvesting chlorophyll a/b binding (LHC) proteins are members of an extended CAB/ELIP/HLIP superfamily of distantly related polypeptides, which have between one and four transmembrane helices (TMH). This superfamily includes the single TMH, high-light-inducible proteins (Hlips), found in cyanobacteria that are induced by various stress conditions, including high light, and are considered ancestral to the LHC proteins. The roles of, and evolutionary relationships between, these superfamily members are of particular interest, since they function in both light harvesting and photoprotection and may have evolved through tandem gene duplication and fusion events. We have investigated the Hlips (hli gene family) in the thermophilic unicellular cyanobacterium Synechococcus OS-B'. The five hli genes present on the genome of Synechococcus OS-B' are relatively similar, but transcript analyses indicate that there are different patterns of transcript accumulation when the cells are exposed to various growth conditions, suggesting that different Hlips may have specific functions. Hlip5 has an additional TMH at the N-terminus as a result of a novel fusion event. This additional TMH is very similar to a conserved hypothetical, single membrane-spanning polypeptide present in most cyanobacteria. The evolutionary significance of these results is discussed.
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Affiliation(s)
- Oliver Kilian
- Department of Plant Biology, The Carnegie Institution, Stanford, CA 94305, USA
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