1
|
Canizales S, Chen PH, Temmink H, Wijffels RH, Janssen M. Cyanobacteria cultivation on human urine for nutrients recovery. ALGAL RES 2023. [DOI: 10.1016/j.algal.2023.103064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
|
2
|
Hackl T, Laurenceau R, Ankenbrand MJ, Bliem C, Cariani Z, Thomas E, Dooley KD, Arellano AA, Hogle SL, Berube P, Leventhal GE, Luo E, Eppley JM, Zayed AA, Beaulaurier J, Stepanauskas R, Sullivan MB, DeLong EF, Biller SJ, Chisholm SW. Novel integrative elements and genomic plasticity in ocean ecosystems. Cell 2023; 186:47-62.e16. [PMID: 36608657 DOI: 10.1016/j.cell.2022.12.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 09/16/2022] [Accepted: 12/05/2022] [Indexed: 01/07/2023]
Abstract
Horizontal gene transfer accelerates microbial evolution. The marine picocyanobacterium Prochlorococcus exhibits high genomic plasticity, yet the underlying mechanisms are elusive. Here, we report a novel family of DNA transposons-"tycheposons"-some of which are viral satellites while others carry cargo, such as nutrient-acquisition genes, which shape the genetic variability in this globally abundant genus. Tycheposons share distinctive mobile-lifecycle-linked hallmark genes, including a deep-branching site-specific tyrosine recombinase. Their excision and integration at tRNA genes appear to drive the remodeling of genomic islands-key reservoirs for flexible genes in bacteria. In a selection experiment, tycheposons harboring a nitrate assimilation cassette were dynamically gained and lost, thereby promoting chromosomal rearrangements and host adaptation. Vesicles and phage particles harvested from seawater are enriched in tycheposons, providing a means for their dispersal in the wild. Similar elements are found in microbes co-occurring with Prochlorococcus, suggesting a common mechanism for microbial diversification in the vast oligotrophic oceans.
Collapse
Affiliation(s)
- Thomas Hackl
- Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA; Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9700CC Groningen, the Netherlands.
| | - Raphaël Laurenceau
- Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA
| | - Markus J Ankenbrand
- Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA; University of Würzburg, Center for Computational and Theoretical Biology, 97070 Würzburg, Germany
| | - Christina Bliem
- Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA
| | - Zev Cariani
- Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA
| | - Elaina Thomas
- Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA
| | - Keven D Dooley
- Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA
| | - Aldo A Arellano
- Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA
| | - Shane L Hogle
- Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA
| | - Paul Berube
- Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA
| | - Gabriel E Leventhal
- Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA
| | - Elaine Luo
- Daniel K. Inouye Center for Microbial Oceanography, Research and Education, University of Hawai'i Manoa, Honolulu, HI 96822, USA
| | - John M Eppley
- Daniel K. Inouye Center for Microbial Oceanography, Research and Education, University of Hawai'i Manoa, Honolulu, HI 96822, USA
| | - Ahmed A Zayed
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA; Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | | | | | - Matthew B Sullivan
- Department of Microbiology & Department of Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA; EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA; Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography, Research and Education, University of Hawai'i Manoa, Honolulu, HI 96822, USA
| | - Steven J Biller
- Wellesley College, Department of Biological Sciences, Wellesley, MA 02481, USA
| | - Sallie W Chisholm
- Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA; Massachusetts Institute of Technology, Department of Biology, Cambridge, MA 02139, USA.
| |
Collapse
|
3
|
Hackl T, Laurenceau R, Ankenbrand MJ, Bliem C, Cariani Z, Thomas E, Dooley KD, Arellano AA, Hogle SL, Berube P, Leventhal GE, Luo E, Eppley JM, Zayed AA, Beaulaurier J, Stepanauskas R, Sullivan MB, DeLong EF, Biller SJ, Chisholm SW. Novel integrative elements and genomic plasticity in ocean ecosystems. Cell 2023. [DOI: doi.org/10.1016/j.cell.2022.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
4
|
Song X, Lin S, Hu Z, Liu Y, Deng Y, Tang YZ. Possible functions of CobW domain-containing (CBWD) genes in dinoflagellates using Karlodinium veneficum as a representative. HARMFUL ALGAE 2022; 117:102274. [PMID: 35944961 DOI: 10.1016/j.hal.2022.102274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 05/30/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Since > 91% of dinoflagellates are proven auxotrophs of vitamin B12 and the cobalamin synthetase W (CobW) is a key gene involved in vitamin B12 synthesis pathway, a number of CobW domain-containing (CBWD) genes in dinoflagellates (DinoCBWDs) were surprisedly found from our transcriptomic and meta-transcriptomic studies. A total of 88 DinoCBWD genes were identified from the genomes and transcriptomes of four dinoflagellates, with five being cloned for full-lengths and characterized using the cosmopolitan and ecologically-important dinoflagellates Karlodinium veneficum and Scrippsiella trochoidea (synonym of Scrippsiella acuminata). DinoCBWDs were verified being irrelevant to vitamin B12 biosynthesis due to their transcriptions irresponsive to vitamin B12 levels and their phylogenetic positions. A comprehensive phylogenetic analysis demonstrated 75 out of the 88 DinoCBWD genes identified belong to three subfamilies of COG0523 protein family, of which most prokaryotic members are reported to be metallochaperones and the eukaryotic members are ubiquitously found but mostly unknown for their functions. Our results from K. veneficum demonstrated DinoCBWDs are associated with metal homeostasis and other divergent functions, with four KvCBWDs involving in zinc homeostasis and KvCBWD1 likely functioning as Fe-type nitrile hydratase activator. In addition, conserved motif analysis revealed the structural foundation of KvCBWD proteins that are consistent with previously described CBWD proteins with GTPase activity and metal binding. Our results provide a stepping-stone toward better understanding the functions of DinoCBWDs and the COG0523 family.
Collapse
Affiliation(s)
- Xiaoying Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Siheng Lin
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhangxi Hu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yuyang Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yunyan Deng
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Ying Zhong Tang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
| |
Collapse
|
5
|
Mikhaylina A, Ksibe AZ, Wilkinson RC, Smith D, Marks E, Coverdale JPC, Fülöp V, Scanlan DJ, Blindauer CA. A single sensor controls large variations in zinc quotas in a marine cyanobacterium. Nat Chem Biol 2022; 18:869-877. [PMID: 35681030 PMCID: PMC9337993 DOI: 10.1038/s41589-022-01051-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/05/2022] [Indexed: 11/09/2022]
Abstract
Marine cyanobacteria are critical players in global nutrient cycles that crucially depend on trace metals in metalloenzymes, including zinc for CO2 fixation and phosphorus acquisition. How strains proliferating in the vast oligotrophic ocean gyres thrive at ultra-low zinc concentrations is currently unknown. Using Synechococcus sp. WH8102 as a model we show that its zinc-sensor protein Zur differs from all other known bacterial Zur proteins in overall structure and the location of its sensory zinc site. Uniquely, Synechococcus Zur activates metallothionein gene expression, which supports cellular zinc quotas spanning two orders of magnitude. Thus, a single zinc sensor facilitates growth across pico- to micromolar zinc concentrations with the bonus of banking this precious resource. The resultant ability to grow well at both ultra-low and excess zinc, together with overall lower zinc requirements, likely contribute to the broad ecological distribution of Synechococcus across the global oceans. ![]()
The zinc-sensor protein Zur in a marine cyanobacterium is distinct from those in other bacteria in structure and location of its sensory zinc site, and facilitates growth across a range of zinc concentrations via activation of a metallothionein gene.
Collapse
Affiliation(s)
- Alevtina Mikhaylina
- Department of Chemistry, University of Warwick, Coventry, UK.,School of Life Sciences, University of Warwick, Coventry, UK
| | - Amira Z Ksibe
- Department of Chemistry, University of Warwick, Coventry, UK.,School of Life Sciences, University of Warwick, Coventry, UK
| | - Rachael C Wilkinson
- School of Life Sciences, University of Warwick, Coventry, UK.,Swansea University Medical School, Swansea, UK
| | - Darbi Smith
- Department of Chemistry, University of Warwick, Coventry, UK
| | - Eleanor Marks
- Department of Chemistry, University of Warwick, Coventry, UK
| | - James P C Coverdale
- Department of Chemistry, University of Warwick, Coventry, UK.,School of Pharmacy, Institute of Clinical Sciences, University of Birmingham, Birmingham, UK
| | - Vilmos Fülöp
- School of Life Sciences, University of Warwick, Coventry, UK
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, UK
| | | |
Collapse
|
6
|
Chakdar H, Thapa S, Srivastava A, Shukla P. Genomic and proteomic insights into the heavy metal bioremediation by cyanobacteria. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127609. [PMID: 34772552 DOI: 10.1016/j.jhazmat.2021.127609] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/16/2021] [Accepted: 10/24/2021] [Indexed: 06/13/2023]
Abstract
Heavy metals (HMs) pose a global ecological threat due to their toxic effects on aquatic and terrestrial life. Effective remediation of HMs from the environment can help to restore soil's fertility and ecological vigor, one of the key Sustainable Development Goals (SDG) set by the United Nations. The cyanobacteria have emerged as a potential option for bioremediation of HMs due to their unique adaptations and robust metabolic machineries. Generally, cyanobacteria deploy multifarious mechanisms such as biosorption, bioaccumulation, activation of metal transporters, biotransformation and induction of detoxifying enzymes to sequester and minimize the toxic effects of heavy metals. Therefore, understanding the physiological responses and regulation of adaptation mechanisms at molecular level is necessary to unravel the candidate genes and proteins which can be manipulated to improve the bioremediation efficiency of cyanobacteria. Chaperons, cellular metabolites (extracellular polymers, biosurfactants), transcriptional regulators, metal transporters, phytochelatins and metallothioneins are some of the potential targets for strain engineering. In the present review, we have discussed the potential of cyanobacteria for HM bioremediation and provided a deeper insight into their genomic and proteomic regulation of various tolerance mechanisms. These approaches might pave new possibilities of implementing genetic engineering strategies for improving bioremediation efficiency with a future perspective.
Collapse
Affiliation(s)
- Hillol Chakdar
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau 275103, Uttar Pradesh, India
| | - Shobit Thapa
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau 275103, Uttar Pradesh, India
| | - Amit Srivastava
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, ID 47907-2048, United States
| | - Pratyoosh Shukla
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India; Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India.
| |
Collapse
|
7
|
Mikhaylina A, Scott L, Scanlan DJ, Blindauer CA. A metallothionein from an open ocean cyanobacterium removes zinc from the sensor protein controlling its transcription. J Inorg Biochem 2022; 230:111755. [DOI: 10.1016/j.jinorgbio.2022.111755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 02/05/2022] [Accepted: 02/06/2022] [Indexed: 10/19/2022]
|
8
|
Ford BA, Sullivan GJ, Moore L, Varkey D, Zhu H, Ostrowski M, Mabbutt BC, Paulsen IT, Shah BS. Functional characterisation of substrate-binding proteins to address nutrient uptake in marine picocyanobacteria. Biochem Soc Trans 2021; 49:2465-2481. [PMID: 34882230 PMCID: PMC8786288 DOI: 10.1042/bst20200244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/03/2021] [Accepted: 11/16/2021] [Indexed: 12/05/2022]
Abstract
Marine cyanobacteria are key primary producers, contributing significantly to the microbial food web and biogeochemical cycles by releasing and importing many essential nutrients cycled through the environment. A subgroup of these, the picocyanobacteria (Synechococcus and Prochlorococcus), have colonised almost all marine ecosystems, covering a range of distinct light and temperature conditions, and nutrient profiles. The intra-clade diversities displayed by this monophyletic branch of cyanobacteria is indicative of their success across a broad range of environments. Part of this diversity is due to nutrient acquisition mechanisms, such as the use of high-affinity ATP-binding cassette (ABC) transporters to competitively acquire nutrients, particularly in oligotrophic (nutrient scarce) marine environments. The specificity of nutrient uptake in ABC transporters is primarily determined by the peripheral substrate-binding protein (SBP), a receptor protein that mediates ligand recognition and initiates translocation into the cell. The recent availability of large numbers of sequenced picocyanobacterial genomes indicates both Synechococcus and Prochlorococcus apportion >50% of their transport capacity to ABC transport systems. However, the low degree of sequence homology among the SBP family limits the reliability of functional assignments using sequence annotation and prediction tools. This review highlights the use of known SBP structural representatives for the uptake of key nutrient classes by cyanobacteria to compare with predicted SBP functionalities within sequenced marine picocyanobacteria genomes. This review shows the broad range of conserved biochemical functions of picocyanobacteria and the range of novel and hypothetical ABC transport systems that require further functional characterisation.
Collapse
Affiliation(s)
- Benjamin A. Ford
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | | | - Lisa Moore
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Deepa Varkey
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Hannah Zhu
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Martin Ostrowski
- Climate Change Cluster (C3), University of Technology Sydney, Sydney, Australia
| | - Bridget C. Mabbutt
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Ian T. Paulsen
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Bhumika S. Shah
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| |
Collapse
|
9
|
Riediger M, Hernández-Prieto MA, Song K, Hess WR, Futschik ME. Genome-wide identification and characterization of Fur-binding sites in the cyanobacteria Synechocystis sp. PCC 6803 and PCC 6714. DNA Res 2021; 28:6407143. [PMID: 34672328 PMCID: PMC8634477 DOI: 10.1093/dnares/dsab023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/16/2021] [Indexed: 11/16/2022] Open
Abstract
The Ferric uptake regulator (Fur) is crucial to both pathogenic and non-pathogenic bacteria for the maintenance of iron homeostasis as well as the defence against reactive oxygen species. Based on datasets from the genome-wide mapping of transcriptional start sites and transcriptome data, we identified a high confidence regulon controlled by Fur for the model cyanobacterium Synechocystis sp. PCC 6803 and its close relative, strain 6714, based on the conserved strong iron starvation response and Fur-binding site occurrence. This regulon comprises 33 protein-coding genes and the sRNA IsaR1 that are under the control of 16 or 14 individual promoters in strains 6803 and 6714, respectively. The associated gene functions are mostly restricted to transporters and enzymes involved in the uptake and storage of iron ions, with few exceptions or unknown functional relevance. Within the isiABC operon, we identified a previously neglected gene encoding a small cysteine-rich protein, which we suggest calling, IsiE. The regulation of iron uptake, storage, and utilization ultimately results from the interplay between the Fur regulon, several other transcription factors, the FtsH3 protease, and the sRNA IsaR1.
Collapse
Affiliation(s)
- Matthias Riediger
- Institute of Biology III, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Miguel A Hernández-Prieto
- ARC Centre of Excellence for Translational Photosynthesis & School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Kuo Song
- Institute of Biology III, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Wolfgang R Hess
- Institute of Biology III, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Matthias E Futschik
- SysBioLab, Centre of Marine Sciences (CCMAR), University of Algarve, 8005-139 Faro, Portugal.,MRC London Institute of Medical Sciences (LMS), Faculty of Medicine, Imperial College London, London W12 0NN, UK
| |
Collapse
|
10
|
Sarker I, Moore LR, Tetu SG. Investigating zinc toxicity responses in marine Prochlorococcus and Synechococcus. MICROBIOLOGY-SGM 2021; 167. [PMID: 34170816 PMCID: PMC8374608 DOI: 10.1099/mic.0.001064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Marine plastic pollution is a growing concern worldwide and has the potential to impact marine life via leaching of chemicals, with zinc (Zn), a common plastic additive, observed at particularly high levels in plastic leachates in previous studies. At this time, however, little is known regarding how elevated Zn affects key groups of marine primary producers. Marine cyanobacterial genera Prochlorococcus and Synechococcus are considered to be some of the most abundant oxygenic phototrophs on earth, and together contribute significantly to oceanic primary productivity. Here we set out to investigate how two Prochlorococcus (MIT9312 and NATL2A) and two Synechococcus (CC9311 and WH8102) strains, representative of diverse ecological niches, respond to exposure to high Zn concentrations. The two genera showed differences in the timing and degree of growth and physiological responses to elevated Zn levels, with Prochlorococcus strains showing declines in their growth rate and photophysiology following exposure to 27 µg l-1 Zn, while Synechococcus CC9311 and WH8102 growth rates declined significantly on exposure to 52 and 152 µg l-1 Zn, respectively. Differences were also observed in each strain's capacity to maintain cell wall integrity on exposure to different levels of Zn. Our results indicate that excess Zn has the potential to pose a challenge to some marine picocyanobacteria and highlights the need to better understand how different marine Prochlorococcus and Synechococcus strains may respond to increasing concentrations of Zn in some marine regions.
Collapse
Affiliation(s)
- Indrani Sarker
- Department of Molecular Sciences, Macquarie University, Sydney, Australia.,MQ Biomolecular Discovery Research Centre, Macquarie University, Sydney, Australia
| | - Lisa R Moore
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Sasha G Tetu
- Department of Molecular Sciences, Macquarie University, Sydney, Australia.,MQ Biomolecular Discovery Research Centre, Macquarie University, Sydney, Australia
| |
Collapse
|
11
|
Huang L, Zuo Y, Qin Y, Zhao L, Lin M, Yan Q. The Zinc Nutritional Immunity of Epinephelus coioides Contributes to the Importance of znuC During Pseudomonas plecoglossicida Infection. Front Immunol 2021; 12:678699. [PMID: 34017347 PMCID: PMC8129501 DOI: 10.3389/fimmu.2021.678699] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 04/19/2021] [Indexed: 12/25/2022] Open
Abstract
Previously, the dual RNA-seq was carried out in a Pseudomonas plecoglossicida- Epinephelus coioides infection model to investigate the dynamics of pathogen-host interplay in vivo. ZnuC, a member of ZnuCBA Zn importer, was found transcriptionally up-regulated during infection. Thus, this study aimed to assess its role during the trade-off for Zn between host and P. plecoglossicida. ICP-MS analysis and fluorescent staining showed that Zn was withheld from serum and accumulated in the spleen, with increased Zn uptake in the Golgi apparatus of macrophages after infection. Additionally, growth assay, macrophage infection and animal infection after gene knockout / silencing revealed that znuC was necessary for growth in Zn-limiting conditions, colonization, intracellular viability, immune escape and virulence of P. plecoglossicida. Further analysis with dual RNA-seq revealed associations of host's Zn nutritional immunity genes with bacterial Zn assimilation genes. IL6 and ZIP4 played key roles in this network, and markedly affected znuB expression, intracellular viability and immune escape, as revealed by gene silencing. Moreover, EMSA and GFP reporter gene analysis showed that Fur sensed changes in Fe concentration to regulate znuCBA in P. plecoglossicida. Jointly, these findings suggest a trade-off for Zn between host and P. plecoglossicida, while ZnuC is important for P. plecoglossicida Zn acquisition.
Collapse
Affiliation(s)
- Lixing Huang
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, China
- Fisheries College, Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Jimei University, Xiamen, China
| | - Yanfei Zuo
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, China
| | - Yingxue Qin
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, China
| | - Lingmin Zhao
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, China
| | - Mao Lin
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, China
| | - Qingpi Yan
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, China
| |
Collapse
|
12
|
Lu T, Zhang Q, Zhang Z, Hu B, Chen J, Chen J, Qian H. Pollutant toxicology with respect to microalgae and cyanobacteria. J Environ Sci (China) 2021; 99:175-186. [PMID: 33183695 DOI: 10.1016/j.jes.2020.06.033] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/24/2020] [Accepted: 06/28/2020] [Indexed: 05/11/2023]
Abstract
Microalgae and cyanobacteria are fundamental components of aquatic ecosystems. Pollution in aquatic environment is a worldwide problem. Toxicological research on microalgae and cyanobacteria can help to establish a solid foundation for aquatic ecotoxicological assessments. Algae and cyanobacteria occupy a large proportion of the biomass in aquatic environments; thus, their toxicological responses have been investigated extensively. However, the depth of toxic mechanisms and breadth of toxicological investigations need to be improved. While existing pollutants are being discharged into the environment daily, new ones are also being produced continuously. As a result, the phenomenon of water pollution has become unprecedentedly complex. In this review, we summarize the latest findings on five kinds of aquatic pollutants, namely, metals, nanomaterials, pesticides, pharmaceutical and personal care products (PPCPs), and persistent organic pollutants (POPs). Further, we present information on emerging pollutants such as graphene, microplastics, and ionic liquids. Efforts in studying the toxicological effects of pollutants on microalgae and cyanobacteria must be increased in order to better predict the potential risks posed by these materials to aquatic ecosystems as well as human health.
Collapse
Affiliation(s)
- Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Jianmeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jun Chen
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China.
| |
Collapse
|
13
|
Vicente A, Sohm B, Flayac J, Rousselle P, Bauda P, Pagnout C. Toxicity mechanisms of ZnO UV-filters used in sunscreens toward the model cyanobacteria Synechococcus elongatus PCC 7942. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:22450-22463. [PMID: 31161548 DOI: 10.1007/s11356-019-05057-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/01/2019] [Indexed: 06/09/2023]
Abstract
Zinc oxide (ZnO) nanoparticles are commonly used in sunscreens for their UV-filtering properties. Their growing use can lead to their release into ecosystems, raising question about their toxicity. Effects of these engineered nanomaterials (ENMs) on cyanobacteria, which are important primary producers involved in many biogeochemical cycles, are unknown. In this study, we investigated by several complementary approaches the toxicological effects of two marketed ZnO-ENMs (coated and uncoated) on the model cyanobacteria Synechococcus elongatus PCC 7942. It was shown that despite the rapid adsorption of ENMs on cell surface, toxicity is mainly due to labile Zn released by ENMs. Zn dissipates cell membrane potential necessary for both photosynthesis and respiration, and induces oxidative stress leading to lipid peroxidation and DNA damages. It leads to global downregulation of photosystems, oxidative phosphorylation, and transcription/translation machineries. This also translates into significant decrease of intracellular ATP content and cell growth inhibition. However, there is no major loss of pigments and even rather an increase in exposed cells compared to controls. A proposed way to reduce the environmental impact of Zn would be the improvement of the coating stability to prevent solubility of ZnO-ENMs.
Collapse
Affiliation(s)
- Anne Vicente
- Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), UMR CNRS 7360, Université de Lorraine, Campus Bridoux, Rue du Général Delestraint, 57070, Metz, France
| | - Bénédicte Sohm
- Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), UMR CNRS 7360, Université de Lorraine, Campus Bridoux, Rue du Général Delestraint, 57070, Metz, France
| | - Justine Flayac
- CNRS, LIEC, UMR7360, Campus Bridoux, 57070, Metz, France
| | - Philippe Rousselle
- Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), UMR CNRS 7360, Université de Lorraine, Campus Bridoux, Rue du Général Delestraint, 57070, Metz, France
| | - Pascale Bauda
- Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), UMR CNRS 7360, Université de Lorraine, Campus Bridoux, Rue du Général Delestraint, 57070, Metz, France
- CNRS, LIEC, UMR7360, Campus Bridoux, 57070, Metz, France
| | - Christophe Pagnout
- Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), UMR CNRS 7360, Université de Lorraine, Campus Bridoux, Rue du Général Delestraint, 57070, Metz, France.
- CNRS, LIEC, UMR7360, Campus Bridoux, 57070, Metz, France.
| |
Collapse
|
14
|
Emergence of metal selectivity and promiscuity in metalloenzymes. J Biol Inorg Chem 2019; 24:517-531. [DOI: 10.1007/s00775-019-01667-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 05/13/2019] [Indexed: 01/27/2023]
|
15
|
Pernil R, Schleiff E. Metalloproteins in the Biology of Heterocysts. Life (Basel) 2019; 9:E32. [PMID: 30987221 PMCID: PMC6616624 DOI: 10.3390/life9020032] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/18/2019] [Accepted: 03/28/2019] [Indexed: 12/15/2022] Open
Abstract
Cyanobacteria are photoautotrophic microorganisms present in almost all ecologically niches on Earth. They exist as single-cell or filamentous forms and the latter often contain specialized cells for N₂ fixation known as heterocysts. Heterocysts arise from photosynthetic active vegetative cells by multiple morphological and physiological rearrangements including the absence of O₂ evolution and CO₂ fixation. The key function of this cell type is carried out by the metalloprotein complex known as nitrogenase. Additionally, many other important processes in heterocysts also depend on metalloproteins. This leads to a high metal demand exceeding the one of other bacteria in content and concentration during heterocyst development and in mature heterocysts. This review provides an overview on the current knowledge of the transition metals and metalloproteins required by heterocysts in heterocyst-forming cyanobacteria. It discusses the molecular, physiological, and physicochemical properties of metalloproteins involved in N₂ fixation, H₂ metabolism, electron transport chains, oxidative stress management, storage, energy metabolism, and metabolic networks in the diazotrophic filament. This provides a detailed and comprehensive picture on the heterocyst demands for Fe, Cu, Mo, Ni, Mn, V, and Zn as cofactors for metalloproteins and highlights the importance of such metalloproteins for the biology of cyanobacterial heterocysts.
Collapse
Affiliation(s)
- Rafael Pernil
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Straβe 9, 60438 Frankfurt am Main, Germany.
| | - Enrico Schleiff
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Straβe 9, 60438 Frankfurt am Main, Germany.
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, 60438 Frankfurt am Main, Germany.
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Straβe 15, 60438 Frankfurt am Main, Germany.
| |
Collapse
|
16
|
Wang Y, Weisenhorn E, MacDiarmid CW, Andreini C, Bucci M, Taggart J, Banci L, Russell J, Coon JJ, Eide DJ. The cellular economy of the Saccharomyces cerevisiae zinc proteome. Metallomics 2018; 10:1755-1776. [PMID: 30358795 PMCID: PMC6291366 DOI: 10.1039/c8mt00269j] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Zinc is an essential cofactor for many proteins. A key mechanism of zinc homeostasis during deficiency is "zinc sparing" in which specific zinc-binding proteins are repressed to reduce the cellular requirement. In this report, we evaluated zinc sparing across the zinc proteome of Saccharomyces cerevisiae. The yeast zinc proteome of 582 known or potential zinc-binding proteins was identified using a bioinformatics analysis that combined global domain searches with local motif searches. Protein abundance was determined by mass spectrometry. In zinc-replete cells, we detected over 2500 proteins among which 229 were zinc proteins. Based on copy number estimates and binding stoichiometries, a replete cell contains ∼9 million zinc-binding sites on proteins. During zinc deficiency, many zinc proteins decreased in abundance and the zinc-binding requirement decreased to ∼5 million zinc atoms per cell. Many of these effects were due at least in part to changes in mRNA levels rather than simply protein degradation. Measurements of cellular zinc content showed that the level of zinc atoms per cell dropped from over 20 million in replete cells to only 1.7 million in deficient cells. These results confirmed the ability of replete cells to store excess zinc and suggested that the majority of zinc-binding sites on proteins in deficient cells are either unmetalated or mismetalated. Our analysis of two abundant zinc proteins, Fba1 aldolase and Met6 methionine synthetase, supported that hypothesis. Thus, we have discovered widespread zinc sparing mechanisms and obtained evidence of a high accumulation of zinc proteins that lack their cofactor during deficiency.
Collapse
Affiliation(s)
- Yirong Wang
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Bacterial zinc uptake regulator proteins and their regulons. Biochem Soc Trans 2018; 46:983-1001. [PMID: 30065104 PMCID: PMC6103462 DOI: 10.1042/bst20170228] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 06/25/2018] [Accepted: 06/26/2018] [Indexed: 01/10/2023]
Abstract
All organisms must regulate the cellular uptake, efflux, and intracellular trafficking of essential elements, including d-block metal ions. In bacteria, such regulation is achieved by the action of metal-responsive transcriptional regulators. Among several families of zinc-responsive transcription factors, the ‘zinc uptake regulator’ Zur is the most widespread. Zur normally represses transcription in its zinc-bound form, in which DNA-binding affinity is enhanced allosterically. Experimental and bioinformatic searches for Zur-regulated genes have revealed that in many cases, Zur proteins govern zinc homeostasis in a much more profound way than merely through the expression of uptake systems. Zur regulons also comprise biosynthetic clusters for metallophore synthesis, ribosomal proteins, enzymes, and virulence factors. In recognition of the importance of zinc homeostasis at the host–pathogen interface, studying Zur regulons of pathogenic bacteria is a particularly active current research area.
Collapse
|
18
|
Peng J, Miao L, Chen X, Liu P. Comparative Transcriptome Analysis of Pseudomonas putida KT2440 Revealed Its Response Mechanisms to Elevated Levels of Zinc Stress. Front Microbiol 2018; 9:1669. [PMID: 30087671 PMCID: PMC6066579 DOI: 10.3389/fmicb.2018.01669] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 07/04/2018] [Indexed: 01/03/2023] Open
Abstract
The whole-genome transcriptional response of Pseudomonas putida KT2440 to stress-inducing concentrations of zinc was analyzed in this study by RNA sequencing to thoroughly investigate the bacterial cell response to zinc toxicity. The data revealed that different levels of zinc stress strongly affected the transcription of genes from the following categories: metal transport genes, genes involved in membrane homeostasis, oxidative-stress-responding genes, and genes associated with basic cellular metabolism. At the lowest zinc dose, only several genes associated with metal transport and membrane homeostasis were strongly influenced. At the intermediate zinc dose, transcriptional changes of genes belonging to these two categories were highly pronounced. In addition, the intermediate zinc stress produced high levels of oxidative stress, and influenced amino acid metabolism and respiratory chains of P. putida. At the highest zinc dose, the induction of genes responsible for Fe–S cluster biogenesis was the most remarkable feature. Moreover, upregulation of glyoxylate cycle was observed. In summary, the adaptation of the cell envelope, the maintenance of metal homeostasis and intracellular redox status, and the transcriptional control of metabolism are the main elements of stress response, which facilitates the survival of P. putida KT2440 in zinc-polluted environments.
Collapse
Affiliation(s)
- Jun Peng
- College of Biological and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Lihong Miao
- College of Biological and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Xi Chen
- Wuhan Institute of Virology, Chinese Academy of Science, Wuhan, China
| | - Pulin Liu
- College of Biological and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
| |
Collapse
|
19
|
Transcriptional patterns identify resource controls on the diazotroph Trichodesmium in the Atlantic and Pacific oceans. ISME JOURNAL 2018; 12:1486-1495. [PMID: 29491494 DOI: 10.1038/s41396-018-0087-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 12/31/2017] [Accepted: 01/10/2018] [Indexed: 12/21/2022]
Abstract
The N2-fixing cyanobacterium Trichodesmium is intensely studied because of the control this organism exerts over the cycling of carbon and nitrogen in the low nutrient ocean gyres. Although iron (Fe) and phosphorus (P) bioavailability are thought to be major drivers of Trichodesmium distributions and activities, identifying resource controls on Trichodesmium is challenging, as Fe and P are often organically complexed and their bioavailability to a single species in a mixed community is difficult to constrain. Further, Fe and P geochemistries are linked through the activities of metalloenzymes, such as the alkaline phosphatases (APs) PhoX and PhoA, which are used by microbes to access dissolved organic P (DOP). Here we identified significant correlations between Trichodesmium-specific transcriptional patterns in the North Atlantic (NASG) and North Pacific Subtropical Gyres (NPSG) and patterns in Fe and P biogeochemistry, with the relative enrichment of Fe stress markers in the NPSG, and P stress markers in the NASG. We also observed the differential enrichment of Fe-requiring PhoX transcripts in the NASG and Fe-insensitive PhoA transcripts in the NPSG, suggesting that metalloenzyme switching may be used to mitigate Fe limitation of DOP metabolism in Trichodesmium. This trait may underpin Trichodesmium success across disparate ecosystems.
Collapse
|
20
|
Molecular basis for the integration of environmental signals by FurB from Anabaena sp. PCC 7120. Biochem J 2018; 475:151-168. [DOI: 10.1042/bcj20170692] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/22/2017] [Accepted: 12/04/2017] [Indexed: 12/29/2022]
Abstract
FUR (Ferric uptake regulator) proteins are among the most important families of transcriptional regulators in prokaryotes, often behaving as global regulators. In the cyanobacterium Anabaena PCC 7120, FurB (Zur, Zinc uptake regulator) controls zinc and redox homeostasis through the repression of target genes in a zinc-dependent manner. In vitro, non-specific binding of FurB to DNA elicits protection against oxidative damage and avoids cleavage by deoxyribonuclease I. The present study provides, for the first time, evidence of the influence of redox environment in the interaction of FurB with regulatory zinc and its consequences in FurB–DNA-binding affinity. Calorimetry studies showed that, in addition to one structural Zn(II), FurB is able to bind two additional Zn(II) per monomer and demonstrated the implication of cysteine C93 in regulatory Zn(II) coordination. The interaction of FurB with the second regulatory zinc occurred only under reducing conditions. While non-specific FurB–DNA interaction is Zn(II)-independent, the optimal binding of FurB to target promoters required loading of two regulatory zinc ions. Those results combined with site-directed mutagenesis and gel-shift assays evidenced that the redox state of cysteine C93 conditions the binding of the second regulatory Zn(II) and, in turn, modulates the affinity for a specific DNA target. Furthermore, differential spectroscopy studies showed that cysteine C93 could also be involved in heme coordination by FurB, either as a direct ligand or being located near the binding site. The results indicate that besides controlling zinc homeostasis, FurB could work as a redox-sensing protein probably modifying its zinc and DNA-binding abilities depending upon environmental conditions.
Collapse
|
21
|
Manjunath M, Kanchan A, Ranjan K, Venkatachalam S, Prasanna R, Ramakrishnan B, Hossain F, Nain L, Shivay YS, Rai AB, Singh B. Beneficial cyanobacteria and eubacteria synergistically enhance bioavailability of soil nutrients and yield of okra. Heliyon 2016; 2:e00066. [PMID: 27441245 PMCID: PMC4945968 DOI: 10.1016/j.heliyon.2016.e00066] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 01/12/2016] [Accepted: 01/15/2016] [Indexed: 12/25/2022] Open
Abstract
Microorganisms in the rhizosphere mediate the cycling of nutrients, their enhanced mobilisation and facilitate their uptake, leading to increased root growth, biomass and yield of plants. We examined the promise of beneficial cyanobacteria and eubacteria as microbial inoculants, applied singly or in combination as consortia or biofilms, to improve growth and yields of okra. Interrelationships among the microbial activities and the micro/macro nutrient dynamics in soils and okra yield characteristics were assessed along with the changes in the soil microbiome. A significant effect of microbial inoculation on alkaline phosphatase activity was recorded both at the mid-crop and harvest stages. Microbial biomass carbon values were highest due to the Anabaena sp. - Providencia sp. (CR1 + PR3) application. The yield of okra ranged from 444.6-478.4 g(-1) plant and a positive correlation (0.69) recorded between yield and root weight. The application of Azotobacter led to the highest root weight and yield. The concentration of Zn at mid-crop stage was 60-70% higher in the Azotobacter sp. and Calothrix sp. inoculated soils, as compared to uninoculated control. Iron concentration in soil was more than 2-3 folds higher than control at the mid-crop stage, especially due to the application of Anabaena-Azotobacter biofilm and Azotobacter sp. Both at the mid-crop and harvest stages, the PCR-DGGE profiles of eubacterial communities were similar among the uninoculated control, the Anabaena sp. - Providencia sp. (CW1 + PW5) and the Anabaena-Azotobacter biofilm treatments. Although the profiles of the Azotobacter, Calothrix and CR1 + PR3 treatments were identical at these stages of growth, the profile of CR1 + PR3 was clearly distinguishable. The performance of the inoculants, particularly Calothrix (T6) and consortium of Anabaena and Providencia (CR1 + PR3; T5), in terms of microbiological and nutrient data, along with generation of distinct PCR-DGGE profiles suggested their superiority and emphasized the utility of combining microbiological and molecular tools in the selection of effective microbial inoculants.
Collapse
Affiliation(s)
- Mallappa Manjunath
- Division of Crop Protection, ICAR-Indian Institute of Vegetable Research, Jakhini, Sahanshapur, Varanasi, 221305, Uttar Pradesh, India
| | - Amrita Kanchan
- Division of Microbiology, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Kunal Ranjan
- Division of Microbiology, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Siddarthan Venkatachalam
- Division of Microbiology, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Radha Prasanna
- Division of Microbiology, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | | | - Firoz Hossain
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Lata Nain
- Division of Microbiology, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Yashbir Singh Shivay
- Division of Agronomy, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Awadhesh Bahadur Rai
- Division of Crop Protection, ICAR-Indian Institute of Vegetable Research, Jakhini, Sahanshapur, Varanasi, 221305, Uttar Pradesh, India
| | - Bijendra Singh
- Division of Crop Protection, ICAR-Indian Institute of Vegetable Research, Jakhini, Sahanshapur, Varanasi, 221305, Uttar Pradesh, India
| |
Collapse
|
22
|
Acharya C, Blindauer CA. Unexpected Interactions of the Cyanobacterial Metallothionein SmtA with Uranium. Inorg Chem 2016; 55:1505-15. [DOI: 10.1021/acs.inorgchem.5b02327] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Celin Acharya
- Molecular
Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
| | | |
Collapse
|
23
|
Kaushik MS, Singh P, Tiwari B, Mishra AK. Ferric Uptake Regulator (FUR) protein: properties and implications in cyanobacteria. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-015-1134-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
|
24
|
Martín-Betancor K, Rodea-Palomares I, Muñoz-Martín MA, Leganés F, Fernández-Piñas F. Construction of a self-luminescent cyanobacterial bioreporter that detects a broad range of bioavailable heavy metals in aquatic environments. Front Microbiol 2015; 6:186. [PMID: 25806029 PMCID: PMC4353254 DOI: 10.3389/fmicb.2015.00186] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 02/19/2015] [Indexed: 11/13/2022] Open
Abstract
A self-luminescent bioreporter strain of the unicellular cyanobacterium Synechococcus sp. PCC 7942 was constructed by fusing the promoter region of the smt locus (encoding the transcriptional repressor SmtB and the metallothionein SmtA) to luxCDABE from Photorhabdus luminescens; the sensor smtB gene controlling the expression of smtA was cloned in the same vector. The bioreporter performance was tested with a range of heavy metals and was shown to respond linearly to divalent Zn, Cd, Cu, Co, Hg, and monovalent Ag. Chemical modeling was used to link bioreporter response with metal speciation and bioavailability. Limits of Detection (LODs), Maximum Permissive Concentrations (MPCs) and dynamic ranges for each metal were calculated in terms of free ion concentrations. The ranges of detection varied from 11 to 72 pM for Hg2+ (the ion to which the bioreporter was most sensitive) to 1.54–5.35 μM for Cd2+ with an order of decreasing sensitivity as follows: Hg2+ >> Cu2+ >> Ag+ > Co2+ ≥ Zn2+ > Cd2+. However, the maximum induction factor reached 75-fold in the case of Zn2+ and 56-fold in the case of Cd2+, implying that Zn2+ is the preferred metal in vivo for the SmtB sensor, followed by Cd2+, Ag+ and Cu2+ (around 45–50-fold induction), Hg2+ (30-fold) and finally Co2+ (20-fold). The bioreporter performance was tested in real environmental samples with different water matrix complexity artificially contaminated with increasing concentrations of Zn, Cd, Ag, and Cu, confirming its validity as a sensor of free heavy metal cations bioavailability in aquatic environments.
Collapse
Affiliation(s)
| | | | - M A Muñoz-Martín
- Department of Biology, Universidad Autónoma de Madrid Madrid, Spain
| | | | | |
Collapse
|
25
|
Goswami S, Diengdoh OL, Syiem MB, Pakshirajan K, Kiran MG. Zn(II) and Cu(II) removal byNostoc muscorum: a cyanobacterium isolated from a coal mining pit in Chiehruphi, Meghalaya, India. Can J Microbiol 2015; 61:209-15. [DOI: 10.1139/cjm-2014-0599] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nostoc muscorum was isolated from a coal mining pit in Chiehruphi, Meghalaya, India, and its potential to remove Zn(II) and Cu(II) from media and the various biochemical alterations it undergoes during metal stress were studied. Metal uptake measured as a function of the ions removed by N. muscorum from media supplemented independently with 20 μmol/L ZnSO4and CuSO4established the ability of this cyanobacterium to remove 66% of Zn2+and 71% of Cu2+within 24 h of contact time. Metal binding on the cell surface was found to be the primary mode of uptake, followed by internalization. Within 7 days of contact, Zn2+and Cu2+mediated dissimilar effects on the organism. For instance, although chlorophyll a synthesis was increased by 12% in Zn2+-treated cells, it was reduced by 26% in Cu2+-treated cells. Total protein content remained unaltered in Zn2+-supplemented medium; however, a 15% reduction was noticed upon Cu2+exposure. Copper enhanced both photosynthesis and respiration by 15% and 19%, respectively; in contrast, photosynthesis was unchanged and respiration dropped by 11% upon Zn2+treatment. Inoculum age also influenced metal removal ability. Experiments in the presence of 3-(3,4-dichlorophenyl)-1,1-dimethylurea (a photosynthetic inhibitor), carbonyl cyanide m-chlorophenyl hydrazone (an uncoupler), and exogenous ATP established that metal uptake was energy dependent, and photosynthesis contributed significantly towards the energy pool required to mediate metal removals.
Collapse
Affiliation(s)
- Smita Goswami
- Department of Biochemistry, North-Eastern Hill University, Shillong 793022, Meghalaya, India
| | - Omega L. Diengdoh
- Department of Biochemistry, North-Eastern Hill University, Shillong 793022, Meghalaya, India
| | - Mayashree B. Syiem
- Department of Biochemistry, North-Eastern Hill University, Shillong 793022, Meghalaya, India
| | - Kannan Pakshirajan
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Mothe Gopi Kiran
- Centre for the Environment, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| |
Collapse
|
26
|
Blindauer CA. Advances in the molecular understanding of biological zinc transport. Chem Commun (Camb) 2015; 51:4544-63. [DOI: 10.1039/c4cc10174j] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Recognition of the importance of zinc homeostasis for health has driven a surge in structural data on major zinc-transporting proteins.
Collapse
|
27
|
Huertas MJ, López-Maury L, Giner-Lamia J, Sánchez-Riego AM, Florencio FJ. Metals in cyanobacteria: analysis of the copper, nickel, cobalt and arsenic homeostasis mechanisms. Life (Basel) 2014; 4:865-86. [PMID: 25501581 PMCID: PMC4284471 DOI: 10.3390/life4040865] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 11/27/2014] [Accepted: 12/04/2014] [Indexed: 11/16/2022] Open
Abstract
Traces of metal are required for fundamental biochemical processes, such as photosynthesis and respiration. Cyanobacteria metal homeostasis acquires an important role because the photosynthetic machinery imposes a high demand for metals, making them a limiting factor for cyanobacteria, especially in the open oceans. On the other hand, in the last two centuries, the metal concentrations in marine environments and lake sediments have increased as a result of several industrial activities. In all cases, cells have to tightly regulate uptake to maintain their intracellular concentrations below toxic levels. Mechanisms to obtain metal under limiting conditions and to protect cells from an excess of metals are present in cyanobacteria. Understanding metal homeostasis in cyanobacteria and the proteins involved will help to evaluate the use of these microorganisms in metal bioremediation. Furthermore, it will also help to understand how metal availability impacts primary production in the oceans. In this review, we will focus on copper, nickel, cobalt and arsenic (a toxic metalloid) metabolism, which has been mainly analyzed in model cyanobacterium Synechocystis sp. PCC 6803.
Collapse
Affiliation(s)
- María José Huertas
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-CSIC, Américo Vespucio 49, E-41092 Sevilla, Spain.
| | - Luis López-Maury
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-CSIC, Américo Vespucio 49, E-41092 Sevilla, Spain.
| | - Joaquín Giner-Lamia
- Systems Biology and Bioinformatics Laboratory, IBB-CBME, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.
| | - Ana María Sánchez-Riego
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-CSIC, Américo Vespucio 49, E-41092 Sevilla, Spain.
| | - Francisco Javier Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-CSIC, Américo Vespucio 49, E-41092 Sevilla, Spain.
| |
Collapse
|
28
|
Sein-Echaluce VC, González A, Napolitano M, Luque I, Barja F, Peleato ML, Fillat MF. Zur (FurB) is a key factor in the control of the oxidative stress response inAnabaenasp. PCC 7120. Environ Microbiol 2014; 17:2006-17. [DOI: 10.1111/1462-2920.12628] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 09/05/2014] [Accepted: 09/09/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Violeta C. Sein-Echaluce
- Departamento de Bioquímica y Biología Molecular y Celular; Instituto de Biocomputación y Física de Sistemas Complejos; Universidad de Zaragoza; Zaragoza 50009 Spain
| | - Andrés González
- Departamento de Bioquímica y Biología Molecular y Celular; Instituto de Biocomputación y Física de Sistemas Complejos; Universidad de Zaragoza; Zaragoza 50009 Spain
| | - Mauro Napolitano
- Instituto de Bioquímica Vegetal y Fotosíntesis; CSIC-Universidad de Sevilla; Sevilla E-41092 Spain
| | - Ignacio Luque
- Instituto de Bioquímica Vegetal y Fotosíntesis; CSIC-Universidad de Sevilla; Sevilla E-41092 Spain
| | - Francisco Barja
- Microbiology Unit; Botany and Plant Biology Department; University of Geneva; Ch. Des Embrouchis 10 Jussy-Geneva CH-1254 Switzerland
| | - M. Luisa Peleato
- Departamento de Bioquímica y Biología Molecular y Celular; Instituto de Biocomputación y Física de Sistemas Complejos; Universidad de Zaragoza; Zaragoza 50009 Spain
| | - María F. Fillat
- Departamento de Bioquímica y Biología Molecular y Celular; Instituto de Biocomputación y Física de Sistemas Complejos; Universidad de Zaragoza; Zaragoza 50009 Spain
| |
Collapse
|
29
|
Improved protein overexpression and purification strategies for structural studies of cyanobacterial metal-responsive transcription factor, SmtB from marine Synechococcus sp. PCC 7002. Protein J 2014; 32:626-34. [PMID: 24264463 DOI: 10.1007/s10930-013-9525-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
There are structural and functional differences in SmtB homologs, metal-responsive transcription factors responsible for sensing of excess heavy metal ions in marine and freshwater cyanobacterial strains. The structure of SmtB from freshwater Synechococcus sp. strain PCC 7942 is elucidated with nuclear magnetic resonance (NMR) and crystallography techniques. But knowledge about the functioning of SmtB homologs from marine species is limited till date. To enable NMR spectroscopic studies for investigating structural and functional aspects, modified protocols with higher yields of isotopically labeled SmtB, from marine species like Synechococcus sp. PCC 7002 are essential. In this study, smtB gene was cloned from genome of Synechococcus sp. PCC 7002 and overexpression protocol for recombinant SmtB was standardized in Escherichia coli containing T7 RNA polymerase/promoter system. Further, the protocol for large-scale production, isotope labeling with (15)N, and purification of recombinant SmtB in E. coli BL21(DE3)/pLysS cells was developed. Purified recombinant protein was successfully used for NMR spectroscopy experiments. These results indicate that the overexpression technique now developed is applicable to the structural and functional studies for the proteins being homologous to cyanobacterial SmtB from Synechococcus sp. PCC 7002.
Collapse
|
30
|
Choi S, Bird AJ. Zinc'ing sensibly: controlling zinc homeostasis at the transcriptional level. Metallomics 2014; 6:1198-215. [PMID: 24722954 DOI: 10.1039/c4mt00064a] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Zinc-responsive transcription factors are found in all kingdoms of life and include the transcriptional activators ZntR, SczA, Zap1, bZip19, bZip23, and MTF-1, and transcriptional repressors Zur, AdcR, Loz1, and SmtB. These factors have two defining features; their activity is regulated by zinc and they all play a central role in zinc homeostasis by controlling the expression of genes that directly affect zinc levels or its availability. This review summarizes what is known about the mechanisms by which each of these factors sense changes in intracellular zinc levels and how they control zinc homeostasis through target gene regulation. Other factors that influence zinc ion sensing are also discussed.
Collapse
Affiliation(s)
- Sangyong Choi
- Department of Human Sciences, The Ohio State University, Columbus, OH 43210, USA
| | | |
Collapse
|
31
|
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]
|
32
|
Barnett JP, Scanlan DJ, Blindauer CA. Identification of major zinc-binding proteins from a marine cyanobacterium: insight into metal uptake in oligotrophic environments. Metallomics 2014; 6:1254-68. [DOI: 10.1039/c4mt00048j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The open ocean cyanobacteriumSynechococcussp. WH8102 thrives at extremely low zinc concentrations. Metalloproteomics experiments have identified an outer-membrane bound porin with zinc-binding ability that is upregulated at low zinc levels, suggesting a role for porins in highly efficient zinc uptake.
Collapse
|
33
|
Hudek L, Pearson LA, Michalczyk A, Neilan BA, Ackland ML. Molecular and cellular characterisation of the zinc uptake (Znu) system ofNostoc punctiforme. FEMS Microbiol Ecol 2013; 86:149-71. [DOI: 10.1111/1574-6941.12153] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Revised: 05/17/2013] [Accepted: 05/17/2013] [Indexed: 12/29/2022] Open
Affiliation(s)
- Lee Hudek
- Centre for Cellular and Molecular Biology; School of Life and Environmental Sciences; Deakin University; Burwood; Vic.; Australia
| | - Leanne A. Pearson
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney; NSW; Australia
| | - Agnes Michalczyk
- Centre for Cellular and Molecular Biology; School of Life and Environmental Sciences; Deakin University; Burwood; Vic.; Australia
| | - Brett A. Neilan
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney; NSW; Australia
| | - M. Leigh Ackland
- Centre for Cellular and Molecular Biology; School of Life and Environmental Sciences; Deakin University; Burwood; Vic.; Australia
| |
Collapse
|
34
|
Gledhill M, Hassler CS, Schoemann V. The environmental bioinorganic chemistry of aquatic microbial organisms. Front Microbiol 2013; 4:100. [PMID: 23630522 PMCID: PMC3635032 DOI: 10.3389/fmicb.2013.00100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 04/08/2013] [Indexed: 11/13/2022] Open
Affiliation(s)
- Martha Gledhill
- National Oceanography Centre, School of Ocean and Earth Science, University of Southampton Southampton, UK
| | | | | |
Collapse
|
35
|
Sydor A, Jost M, Ryan KS, Turo KE, Douglas C, Drennan CL, Zamble DB. Metal binding properties of Escherichia coli YjiA, a member of the metal homeostasis-associated COG0523 family of GTPases. Biochemistry 2013; 52:1788-1801. [PMID: 24449932 PMCID: PMC3596956 DOI: 10.1021/bi301600z] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
GTPases are critical molecular switches involved in a wide range of biological functions. Recent phylogenetic and genomic analyses of the large, mostly uncharacterized COG0523 subfamily of GTPases revealed a link between some COG0523 proteins and metal homeostasis pathways. In this report, we detail the bioinorganic characterization of YjiA, a representative member of COG0523 subgroup 9 and the only COG0523 protein to date with high-resolution structural information. We find that YjiA is capable of binding several types of transition metals with dissociation constants in the low micromolar range and that metal binding affects both the oligomeric structure and GTPase activity of the enzyme. Using a combination of X-ray crystallography and site-directed mutagenesis, we identify, among others, a metal-binding site adjacent to the nucleotide-binding site in the GTPase domain that involves a conserved cysteine and several glutamate residues. Mutations of the coordinating residues decrease the impact of metal, suggesting that metal binding to this site is responsible for modulating the GTPase activity of the protein. These findings point toward a regulatory function for these COG0523 GTPases that is responsive to their metal-bound state.
Collapse
Affiliation(s)
- Andrew
M. Sydor
- Department of Chemistry, University
of Toronto, 80 St. George Street, Toronto,
ON, Canada M5S 3H6
| | - Marco Jost
- ‡Department
of Chemistry, §Department of Biology, and ∥Howard Hughes Medical Institute, Massachusetts Institute of Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
| | - Katherine S. Ryan
- ‡Department
of Chemistry, §Department of Biology, and ∥Howard Hughes Medical Institute, Massachusetts Institute of Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
| | - Kaitlyn E. Turo
- ‡Department
of Chemistry, §Department of Biology, and ∥Howard Hughes Medical Institute, Massachusetts Institute of Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
| | - Colin
D. Douglas
- Department of Chemistry, University
of Toronto, 80 St. George Street, Toronto,
ON, Canada M5S 3H6
| | - Catherine L. Drennan
- ‡Department
of Chemistry, §Department of Biology, and ∥Howard Hughes Medical Institute, Massachusetts Institute of Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States,C.L.D.:
telephone, (617)
253-5622; fax, (617) 258-7847; e-mail, . D.B.Z.: telephone, (416) 978-3568; e-mail,
| | - Deborah B. Zamble
- Department of Chemistry, University
of Toronto, 80 St. George Street, Toronto,
ON, Canada M5S 3H6,C.L.D.:
telephone, (617)
253-5622; fax, (617) 258-7847; e-mail, . D.B.Z.: telephone, (416) 978-3568; e-mail,
| |
Collapse
|