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Liu Z, Li Y, Shan S, Zhang M, Yang H, Cheng W, Wei X, Wang Y, Wu S. Regulatory roles of APS reductase in Citrobacter sp. XT1-2-2 as a response mechanism to cadmium immobilization in rice. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 284:116892. [PMID: 39153279 DOI: 10.1016/j.ecoenv.2024.116892] [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: 05/08/2024] [Revised: 07/19/2024] [Accepted: 08/13/2024] [Indexed: 08/19/2024]
Abstract
Citrobacter sp. XT1-2-2, a functional microorganism with potential utilization, has the ability to immobilize soil cadmium. In this study, the regulatory gene cysH, as a rate-limiting enzyme in the sulfur metabolic pathway, was selected for functional analysis affecting cadmium immobilization in soil. To verify the effect of APS reductase on CdS formation, the ΔAPS and ΔAPS-com strains were constructed by conjugation transfer. Through TEM analysis, it was found that the adsorption of Cd2+ was affected by the absence of APS reductase in XT1-2-2 strain. The difference analysis of biofilm formation indicated that APS reductase was necessary for cell aggregation and biofilm formation. The p-XRD, XPS and FT-IR analysis revealed that APS reductase played an important role in the cadmium immobilization process of XT1-2-2 strain and promoting the formation of CdS. According to the pot experiments, the cadmium concentration of roots, culms, leaves and grains inoculated with ΔAPS strain was significantly higher than that of wild-type and ΔAPS-com strains, and the cadmium removal ability of ΔAPS strain was significantly lower than that of wild-type strain. The study provided insights into the exploration of new bacterial assisted technique for the remediation and safe production of rice in cadmium-contaminated paddy soils.
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Affiliation(s)
- Zhudong Liu
- Hunan Institute of Microbiology, Changsha, Hunan 410009, China
| | - Yilu Li
- Hunan Institute of Microbiology, Changsha, Hunan 410009, China
| | - Shiping Shan
- Hunan Institute of Microbiology, Changsha, Hunan 410009, China; Hunan Engineering and Technology Research Center of Agricultural Microbiology Application, Changsha, Hunan 410009, China.
| | - Min Zhang
- Hunan Institute of Microbiology, Changsha, Hunan 410009, China.
| | - Hua Yang
- Hunan Institute of Microbiology, Changsha, Hunan 410009, China.
| | - Wei Cheng
- Hunan Institute of Microbiology, Changsha, Hunan 410009, China
| | - Xiaowu Wei
- Hunan Institute of Microbiology, Changsha, Hunan 410009, China
| | - Yushuang Wang
- Hunan Institute of Microbiology, Changsha, Hunan 410009, China
| | - Shandong Wu
- Hunan Institute of Microbiology, Changsha, Hunan 410009, China
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Kopriva S, Rahimzadeh Karvansara P, Takahashi H. Adaptive modifications in plant sulfur metabolism over evolutionary time. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4697-4711. [PMID: 38841807 PMCID: PMC11350084 DOI: 10.1093/jxb/erae252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/03/2024] [Indexed: 06/07/2024]
Abstract
Sulfur (S) is an essential element for life on Earth. Plants are able to take up and utilize sulfate (SO42-), the most oxidized inorganic form of S compounds on Earth, through the reductive S assimilatory pathway that couples with photosynthetic energy conversion. Organic S compounds are subsequently synthesized in plants and made accessible to animals, primarily as the amino acid methionine. Thus, plant S metabolism clearly has nutritional importance in the global food chain. S metabolites may be part of redox regulation and drivers of essential metabolic pathways as cofactors and prosthetic groups, such as Fe-S centers, CoA, thiamine, and lipoic acid. The evolution of the S metabolic pathways and enzymes reflects the critical importance of functional innovation and diversifications. Here we review the major evolutionary alterations that took place in S metabolism across different scales and outline research directions that may take advantage of understanding the evolutionary adaptations.
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Affiliation(s)
- Stanislav Kopriva
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zülpicher Str. 47b, D-50674 Cologne, Germany
| | - Parisa Rahimzadeh Karvansara
- Institute of Molecular Photosynthesis, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Hideki Takahashi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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3
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Luo W, Zhao M, Dwidar M, Gao Y, Xiang L, Wu X, Medema MH, Xu S, Li X, Schäfer H, Chen M, Feng R, Zhu Y. Microbial assimilatory sulfate reduction-mediated H 2S: an overlooked role in Crohn's disease development. MICROBIOME 2024; 12:152. [PMID: 39152482 PMCID: PMC11328384 DOI: 10.1186/s40168-024-01873-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 07/13/2024] [Indexed: 08/19/2024]
Abstract
BACKGROUND H2S imbalances in the intestinal tract trigger Crohn's disease (CD), a chronic inflammatory gastrointestinal disorder characterized by microbiota dysbiosis and barrier dysfunction. However, a comprehensive understanding of H2S generation in the gut, and the contributions of both microbiota and host to systemic H2S levels in CD, remain to be elucidated. This investigation aimed to enhance comprehension regarding the sulfidogenic potential of both the human host and the gut microbiota. RESULTS Our analysis of a treatment-naive CD cohorts' fecal metagenomic and biopsy metatranscriptomic data revealed reduced expression of host endogenous H2S generation genes alongside increased abundance of microbial exogenous H2S production genes in correlation with CD. While prior studies focused on microbial H2S production via dissimilatory sulfite reductases, our metagenomic analysis suggests the assimilatory sulfate reduction (ASR) pathway is a more significant contributor in the human gut, given its high prevalence and abundance. Subsequently, we validated our hypothesis experimentally by generating ASR-deficient E. coli mutants ∆cysJ and ∆cysM through the deletion of sulfite reductase and L-cysteine synthase genes. This alteration significantly affected bacterial sulfidogenic capacity, colon epithelial cell viability, and colonic mucin sulfation, ultimately leading to colitis in murine model. Further study revealed that gut microbiota degrade sulfopolysaccharides and assimilate sulfate to produce H2S via the ASR pathway, highlighting the role of sulfopolysaccharides in colitis and cautioning against their use as food additives. CONCLUSIONS Our study significantly advances understanding of microbial sulfur metabolism in the human gut, elucidating the complex interplay between diet, gut microbiota, and host sulfur metabolism. We highlight the microbial ASR pathway as an overlooked endogenous H2S producer and a potential therapeutic target for managing CD. Video Abstract.
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Affiliation(s)
- Wanrong Luo
- Department of Gastroenterology, the First Affiliated Hospital, Sun Yat-Sen University, No.58 Zhongshan Er Road, Room 1209, Guangzhou, 510080, China
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Min Zhao
- Department of Gastroenterology, Shenzhen No.3 People's Hospital, Shenzhen, Guangdong, China
| | - Mohammed Dwidar
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA
| | - Yang Gao
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Liyuan Xiang
- Department of Gastroenterology, the First Affiliated Hospital, Sun Yat-Sen University, No.58 Zhongshan Er Road, Room 1209, Guangzhou, 510080, China
| | - Xueting Wu
- Department of Gastroenterology, the First Affiliated Hospital, Sun Yat-Sen University, No.58 Zhongshan Er Road, Room 1209, Guangzhou, 510080, China
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Shu Xu
- Department of Gastroenterology, the First Affiliated Hospital, Sun Yat-Sen University, No.58 Zhongshan Er Road, Room 1209, Guangzhou, 510080, China
| | - Xiaozhi Li
- Department of Gastroenterology, the First Affiliated Hospital, Sun Yat-Sen University, No.58 Zhongshan Er Road, Room 1209, Guangzhou, 510080, China
| | - Hendrik Schäfer
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Minhu Chen
- Department of Gastroenterology, the First Affiliated Hospital, Sun Yat-Sen University, No.58 Zhongshan Er Road, Room 1209, Guangzhou, 510080, China.
| | - Rui Feng
- Department of Gastroenterology, the First Affiliated Hospital, Sun Yat-Sen University, No.58 Zhongshan Er Road, Room 1209, Guangzhou, 510080, China.
| | - Yijun Zhu
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.
- Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-Sen University), Ministry of Education, Guangzhou, Guangdong, China.
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Wang Z, Zhang Y, Chen Y, Han F, Shi Y, Pan S, Li Z. Competition of Cd(II) and Pb(II) on the bacterial cells: a new insight from bioaccumulation based on NanoSIMS imaging. Appl Environ Microbiol 2024; 90:e0145323. [PMID: 38224623 PMCID: PMC10880600 DOI: 10.1128/aem.01453-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/01/2023] [Indexed: 01/17/2024] Open
Abstract
Polymetallic exposure causes complex toxicity to microorganisms. In this study, we investigated the responses of Escherichia coli under co-existence of cadmium (Cd) and lead (Pb), primarily based on biochemical analysis and RNA sequencing. Cd completely inhibited bacterial growth at a concentration of 2.41 mmol/L, with its removal rate as low as <10%. In contrast, the Pb removal rate was >95% under equimolar sole Pb stress. In addition, the Raman analysis confirmed the loss of proteins for the bacterial cells. Under the co-existence of Cd and Pb, the Cd toxicity to E. coli was alleviated. Meanwhile, the biosorption of Pb cations was more intense during the competitive sorption with Cd. Transmission electron microscopy images showed that a few cells were elongated during incubation, i.e., the average cellular length increased from 1.535 ± 0.407 to 1.845 ± 0.620 µm. Moreover, NanoSIMS imaging showed that the intracellular distribution of Cd and Pb was coupled with sulfur. Genes regulating sulfate transporter were also upregulated to promote sulfate assimilation. Then, the subsequent production of biogenic sulfide and sulfur-containing amino acids was enhanced. Although this strategy based on S enrichment could resist the polymetallic stress, not all related genes were induced to upregulate under sole Cd stress. Therefore, the S metabolism might remodel the microbial resistance to variable occurrence of heavy metals. Furthermore, the competitive sorption (in contrast to sole Cd stress) could prevent microbial cells from strong Cd toxicity.IMPORTANCEMicrobial tolerance and resistance to heavy metals have been widely studied under stress of single metals. However, the polymetallic exposure seems to prevail in the environment. Though microbial resistance can alleviate the effects of exogenous stress, the taxonomic or functional response to polymetallic exposure is still not fully understood. We determined the strong cytotoxicity of cadmium (Cd) on growth, and cell elongation would be driven by Cd stress. The addition of appropriate lead (Pb) showed a stimulating effect on microbial bioactivity. Meanwhile, the biosorption of Pb was more intense during co-existence of Pb and Cd. Our work also revealed the spatial coupling of intracellular S and Cd/Pb. In particular, the S assimilation was promoted by Pb stress. This work elucidated the microbial responses to polymetallic exposure and may provide new insights into the antagonistic function during metal stresses.
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Affiliation(s)
- Zhijun Wang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, Guizhou, China.
| | - Ying Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yunhui Chen
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Feiyu Han
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yixiao Shi
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Shang Pan
- College of Agro-grassland Sciences, Nanjing Agricultural University, Nanjing, China
| | - Zhen Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, Guizhou, China.
- Key Laboratory of Eco-geochemistry, Ministry of Natural Resources, Beijing, China
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
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Ishola OA, Kublik S, Durai Raj AC, Ohnmacht C, Schulz S, Foesel BU, Schloter M. Comparative Metagenomic Analysis of Bacteriophages and Prophages in Gnotobiotic Mouse Models. Microorganisms 2024; 12:255. [PMID: 38399658 PMCID: PMC10892684 DOI: 10.3390/microorganisms12020255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
Gnotobiotic murine models are important to understand microbiota-host interactions. Despite the role of bacteriophages as drivers for microbiome structure and function, there is no information about the structure and function of the gut virome in gnotobiotic models and the link between bacterial and bacteriophage/prophage diversity. We studied the virome of gnotobiotic murine Oligo-MM12 (12 bacterial species) and reduced Altered Schaedler Flora (ASF, three bacterial species). As reference, the virome of Specific Pathogen-Free (SPF) mice was investigated. A metagenomic approach was used to assess prophages and bacteriophages in the guts of 6-week-old female mice. We identified a positive correlation between bacteria diversity, and bacteriophages and prophages. Caudoviricetes (82.4%) were the most prominent class of phages in all samples with differing relative abundance. However, the host specificity of bacteriophages belonging to class Caudoviricetes differed depending on model bacterial diversity. We further studied the role of bacteriophages in horizontal gene transfer and microbial adaptation to the host's environment. Analysis of mobile genetic elements showed the contribution of bacteriophages to the adaptation of bacterial amino acid metabolism. Overall, our results implicate virome "dark matter" and interactions with the host system as factors for microbial community structure and function which determine host health. Taking the importance of the virome in the microbiome diversity and horizontal gene transfer, reductions in the virome might be an important factor driving losses of microbial biodiversity and the subsequent dysbiosis of the gut microbiome.
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Affiliation(s)
- Oluwaseun A. Ishola
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany; (O.A.I.)
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany; (O.A.I.)
| | - Abilash Chakravarthy Durai Raj
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany; (O.A.I.)
| | - Caspar Ohnmacht
- Mucosal Immunology Group, Center of Allery and Environment (ZAUM), Technical University of Munich, Helmholtz Zentrum München, 85764 München, Germany
| | - Stefanie Schulz
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany; (O.A.I.)
| | - Bärbel U. Foesel
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany; (O.A.I.)
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany; (O.A.I.)
- Chair for Environmental Microbiology, TUM School of Life Science, Technical University of Munich, 85354 Freising, Germany
- Central Institute for Nutrition and Health, Technical University of Munich, 85354 Freising, Germany
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6
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Tanabe TS, Dahl C. HMSS2: An advanced tool for the analysis of sulphur metabolism, including organosulphur compound transformation, in genome and metagenome assemblies. Mol Ecol Resour 2023; 23:1930-1945. [PMID: 37515475 DOI: 10.1111/1755-0998.13848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/08/2023] [Accepted: 07/17/2023] [Indexed: 07/31/2023]
Abstract
The global sulphur cycle has implications for human health, climate change, biogeochemistry and bioremediation. The organosulphur compounds that participate in this cycle not only represent a vast reservoir of sulphur but are also used by prokaryotes as sources of energy and/or carbon. Closely linked to the inorganic sulphur cycle, it involves the interaction of prokaryotes, eukaryotes and chemical processes. However, ecological and evolutionary studies of the conversion of organic sulphur compounds are hampered by the poor conservation of the relevant pathways and their variation even within strains of the same species. In addition, several proteins involved in the conversion of sulphonated compounds are related to proteins involved in sulphur dissimilation or turnover of other compounds. Therefore, the enzymes involved in the metabolism of organic sulphur compounds are usually not correctly annotated in public databases. To address this challenge, we have developed HMSS2, a profiled Hidden Markov Model-based tool for rapid annotation and synteny analysis of organic and inorganic sulphur cycle proteins in prokaryotic genomes. Compared to its previous version (HMS-S-S), HMSS2 includes several new features. HMM-based annotation is now supported by nonhomology criteria and covers the metabolic pathways of important organosulphur compounds, including dimethylsulphoniopropionate, taurine, isethionate, and sulphoquinovose. In addition, the calculation speed has been increased by a factor of four and the available output formats have been extended to include iTol compatible data sets, and customized sequence FASTA files.
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Affiliation(s)
- Tomohisa Sebastian Tanabe
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
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7
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Zheng K, Dong Y, Liang Y, Liu Y, Zhang X, Zhang W, Wang Z, Shao H, Sung YY, Mok WJ, Wong LL, McMinn A, Wang M. Genomic diversity and ecological distribution of marine Pseudoalteromonas phages. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:271-285. [PMID: 37275543 PMCID: PMC10232697 DOI: 10.1007/s42995-022-00160-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 12/01/2022] [Indexed: 06/07/2023]
Abstract
Pseudoalteromonas, with a ubiquitous distribution, is one of the most abundant marine bacterial genera. It is especially abundant in the deep sea and polar seas, where it has been found to have a broad metabolic capacity and unique co-existence strategies with other organisms. However, only a few Pseudoalteromonas phages have so far been isolated and investigated and their genomic diversity and distribution patterns are still unclear. Here, the genomes, taxonomic features and distribution patterns of Pseudoalteromonas phages are systematically analyzed, based on the microbial and viral genomes and metagenome datasets. A total of 143 complete or nearly complete Pseudoalteromonas-associated phage genomes (PSAPGs) were identified, including 34 Pseudoalteromonas phage isolates, 24 proviruses, and 85 Pseudoalteromonas-associated uncultured viral genomes (UViGs); these were assigned to 47 viral clusters at the genus level. Many integrated proviruses (n = 24) and filamentous phages were detected (n = 32), suggesting the prevalence of viral lysogenic life cycle in Pseudoalteromonas. PSAPGs encoded 66 types of 249 potential auxiliary metabolic genes (AMGs) relating to peptidases and nucleotide metabolism. They may also participate in marine biogeochemical cycles through the manipulation of the metabolism of their hosts, especially in the phosphorus and sulfur cycles. Siphoviral and filamentous PSAPGs were the predominant viral lineages found in polar areas, while some myoviral and siphoviral PSAPGs encoding transposase were more abundant in the deep sea. This study has expanded our understanding of the taxonomy, phylogenetic and ecological scope of marine Pseudoalteromonas phages and deepens our knowledge of viral impacts on Pseudoalteromonas. It will provide a baseline for the study of interactions between phages and Pseudoalteromonas in the ocean. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-022-00160-z.
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Affiliation(s)
- Kaiyang Zheng
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266100 China
| | - Yue Dong
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266100 China
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266100 China
- UMT-OUC Joint Center for Marine Studies, Qingdao, 266003 China
| | - Yundan Liu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266100 China
| | - Xinran Zhang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266100 China
| | - Wenjing Zhang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266100 China
| | - Ziyue Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266100 China
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266100 China
- UMT-OUC Joint Center for Marine Studies, Qingdao, 266003 China
| | - Yeong Yik Sung
- UMT-OUC Joint Center for Marine Studies, Qingdao, 266003 China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), 21030 Kuala Nerus, Malaysia
| | - Wen Jye Mok
- UMT-OUC Joint Center for Marine Studies, Qingdao, 266003 China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), 21030 Kuala Nerus, Malaysia
| | - Li Lian Wong
- UMT-OUC Joint Center for Marine Studies, Qingdao, 266003 China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), 21030 Kuala Nerus, Malaysia
| | - Andrew McMinn
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266100 China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Australia
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266100 China
- UMT-OUC Joint Center for Marine Studies, Qingdao, 266003 China
- Haide College, Ocean University of China, Qingdao, 266100 China
- The Affiliated Hospital of Qingdao University, Qingdao, 266000 China
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8
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Qin J, Ji B, Ma Y, Liu X, Wang T, Liu G, Li B, Wang G, Gao P. Diversity and potential function of pig gut DNA viruses. Heliyon 2023; 9:e14020. [PMID: 36915549 PMCID: PMC10006684 DOI: 10.1016/j.heliyon.2023.e14020] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Viruses are ubiquitous in the gut of animals and play an important role in the ecology of the gut microbiome. The potential effects of these substances on the growth and development of the body are not fully known. Little is known about the effects of breeding environment on pig gut virome. Here, there are 3584 viral operational taxonomic units (vOTUs) longer than 5 kb identified by virus-enriched metagenome sequencing from 25 pig fecal samples. Only a small minority of vOTUs (11.16%) can be classified at the family level, and ∼50% of the genes could be annotated, supporting the concept of pig gut as reservoirs of substantial undescribed viral genetic diversity. The composition of pig gut virome in the six regions may be related to geography. There are only 20 viral clusters (VCs) shared among pig gut virome in six regions of Shanxi Province. These viruses rarely carry antibiotic resistance genes (ARGs). At the same time, they possess abundant auxiliary metabolic genes (AMGs) potentially involved in carbon, sulfur metabolism and cofactor biosynthesis, etc. This study has revealed the unique characteristics and potential function of pig gut DNA virome and established a foundation for the recognition of the viral roles in gut environment.
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Affiliation(s)
- Junjun Qin
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
| | - Bingzhen Ji
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
| | - Yijia Ma
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
| | - Xin Liu
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Tian Wang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Guiming Liu
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Bugao Li
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
| | - Guoliang Wang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Pengfei Gao
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
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9
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Jroundi F, Povedano-Priego C, Pinel-Cabello M, Descostes M, Grizard P, Purevsan B, Merroun ML. Evidence of microbial activity in a uranium roll-front deposit: Unlocking their potential role as bioenhancers of the ore genesis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 861:160636. [PMID: 36464038 DOI: 10.1016/j.scitotenv.2022.160636] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/26/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Uranium (U) roll-front deposits constitute a valuable source for an economical extraction by in situ recovery (ISR) mining. Such technology may induce changes in the subsurface microbiota, raising questions about the way their activities could build a functional ecosystem in such extreme environments (i.e.: oligotrophy and high SO4 concentration and salinity). Additionally, more information is needed to dissipate the doubts about the microbial role in the genesis of such U orebodies. A U roll-front deposit hosted in an aquifer driven system (in Zoovch Ovoo, Mongolia), intended for mining by acid ISR, was previously explored and showed to be governed by a complex bacterial diversity, linked to the redox zonation and the geochemical conditions. Here for the first time, transcriptional activities of microorganisms living in such U ore deposits are determined and their metabolic capabilities allocated in the three redox-inherited compartments, naturally defined by the roll-front system. Several genes encoding for crucial metabolic pathways demonstrated a strong biological role controlling the subsurface cycling of many elements including nitrate, sulfate, metals and radionuclides (e.g.: uranium), through oxidation-reduction reactions. Interestingly, the discovered transcriptional behaviour gives important insights into the good microbial adaptation to the geochemical conditions and their active contribution to the stabilization of the U ore deposits. Overall, evidences on the importance of these microbial metabolic activities in the aquifer system are discussed that may clarify the doubts on the microbial role in the genesis of low-temperature U roll-front deposits, along the Zoovch Ovoo mine.
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Affiliation(s)
- Fadwa Jroundi
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain.
| | - Cristina Povedano-Priego
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain
| | - María Pinel-Cabello
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain
| | - Michael Descostes
- ORANO Mining, 125 Avenue de Paris, 92330 Châtillon, France; Centre de Géosciences, MINES ParisTech, PSL University, 35 rue St Honoré, 77300 Fontainebleau, France
| | - Pierre Grizard
- ORANO Mining, 125 Avenue de Paris, 92330 Châtillon, France
| | - Bayaarma Purevsan
- Badrakh Energy LLC, Jamyan Gun Avenue - 9, Sukhbaatar district, 1st khoroo, UB-14240, Mongolia
| | - Mohamed L Merroun
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain
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10
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Kawakami T, Teramoto T, Kakuta Y. Crystal structure of adenosine 5'-phosphosulfate kinase isolated from Archaeoglobus fulgidus. Biochem Biophys Res Commun 2023; 643:105-110. [PMID: 36592583 DOI: 10.1016/j.bbrc.2022.12.081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022]
Abstract
The 3'-phosphoadenosine-5'-phosphosulfate (PAPS) molecule is essential during enzyme-catalyzed sulfation reactions as a sulfate donor and is an intermediate in the reduction of sulfate to sulfite in the sulfur assimilation pathway. PAPS is produced through a two-step reaction involving ATP sulfurylase and adenosine 5'-phosphosulfate (APS) kinase enzymes/domains. However, archaeal APS kinases have not yet been characterized and their mechanism of action remains unclear. Here, we first structurally characterized APS kinase from the hyperthermophilic archaeon Archaeoglobus fulgidus, (AfAPSK). We demonstrated the PAPS production activity of AfAPSK at the optimal growth temperature (83 °C). Furthermore, we determined the two crystal structures of AfAPSK: ADP complex and ATP analog adenylyl-imidodiphosphate (AMP-PNP)/Mg2+/APS complex. Structural and complementary mutational analyses revealed the catalytic and substrate recognition mechanisms of AfAPSK. This study also hints at the molecular basis behind the thermal stability of AfAPSK.
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Affiliation(s)
- Tomoya Kawakami
- Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Takamasa Teramoto
- Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan.
| | - Yoshimitsu Kakuta
- Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan.
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11
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Yang S, Tang R, Xie CJ, Han S, Rensing C, Liu GH, Zhou SG. A novel sulfate-reducing and nitrogen-fixing bacterium Fundidesulfovibrio soli sp. nov., isolated from paddy soils. Arch Microbiol 2023; 205:80. [PMID: 36735086 DOI: 10.1007/s00203-023-03412-3] [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: 12/13/2022] [Accepted: 01/10/2023] [Indexed: 02/04/2023]
Abstract
A strictly anaerobic sulfate-reducing strain, designated SG60T, was isolated from paddy soil collected in Fujian Province, China. Growth of strain SG60T was observed at 20-37 °C, pH 5.5-10.0 and 0-0.7% (w/v) NaCl. Strain SG60T showed the highest 16S rRNA sequence similarities to the type strains of Fundidesulfovibrio magnetotacticus FSS-1T (97.2%) and Fundidesulfovibrio putealis DSM 16056T (96.4%). Phylogenetic trees based on the16S rRNA sequence and genome-based phylogenomic tree constructed using 120 core genes showed that strain SG60T clustered with members of the genus Fundidesulfovibrio. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain SG60T and the most closely related type strain F. magnetotacticus were 78.2% and 21.6%, respectively. Strain SG60T contained MK-7 as the main respiratory quinone and anteiso-C15:0, anteiso-C17:1 ω9c, iso-C16:0 and iso-C16:1 H as the major fatty acids. Strain SG60T produced desulfoviridin and possessed genes (nifHDK) encoding functions involved in nitrogen fixation. The genomic DNA G + C content was 65.5%. Based on the observed physiological properties, chemotaxonomic characteristics and ANI and dDDH values, strain SG60T represents a novel species of the genus Fundidesulfovibrio, for which the name Fundidesulfovibrio soli sp. nov. is proposed. The type strain is SG60T (= GDMCC 1.3310T = JCM 35676T).
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Affiliation(s)
- Shang Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, 350002, Fujian Province, People's Republic of China
| | - Rong Tang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, 350002, Fujian Province, People's Republic of China
| | - Cheng-Jie Xie
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, 350002, Fujian Province, People's Republic of China
| | - Shuang Han
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, 350002, Fujian Province, People's Republic of China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, 350002, Fujian Province, People's Republic of China
| | - Guo-Hong Liu
- Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou City, 350003, Fujian Province, People's Republic of China.
| | - Shun-Gui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, 350002, Fujian Province, People's Republic of China.
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12
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Pokhrel A, Dinh H, Li L, Hassan KA, Cain AK, Paulsen IT. Identification of a Novel LysR Family Transcriptional Regulator Controlling Acquisition of Sulfur Sources in Acinetobacter baumannii. Microb Physiol 2023; 33:27-35. [PMID: 36626888 DOI: 10.1159/000529038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 12/30/2022] [Indexed: 01/11/2023]
Abstract
l-cysteine biosynthesis from inorganic sulfur represents a major mechanism by which reduced sulfur is incorporated into organic compounds. Cysteine biosynthesis and regulation is well characterized in Escherichia coli. However, the regulation of sulfur metabolism in Acinetobacter baumannii is only partly understood, with the LysR-type regulator, GigC known to control some aspects of sulfur reduction. In this study, we have used transcriptomics and bioinformatic analyses to characterize a novel LysR-type transcriptional regulator encoded by ABUW_1016 (cbl), in a highly multidrug resistant and virulent isolate of A. baumannii. We have shown that Cbl is involved in controlling expression of the genes required for uptake and reduction of various sulfur sources in A. baumannii. Collectively, we have identified the global regulon of Cbl and proposed a model of cysteine biosynthesis and its regulation by Cbl and GigC in A. baumannii.
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Affiliation(s)
- Alaska Pokhrel
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia,
| | - Hue Dinh
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Liping Li
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Karl A Hassan
- School of Environmental and Life Sciences, University of Newcastle, Newcastle, New South Wales, Australia
| | - Amy K Cain
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales, Australia
| | - Ian T Paulsen
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales, Australia
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13
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Xu B, Fan L, Wang W, Zhu Y, Zhang C. Diversity, distribution, and functional potentials of magroviruses from marine and brackish waters. Front Microbiol 2023; 14:1151034. [PMID: 37152742 PMCID: PMC10160649 DOI: 10.3389/fmicb.2023.1151034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/05/2023] [Indexed: 05/09/2023] Open
Abstract
Marine group II (MGII) archaea (Ca. Poseidoniales) are among the most abundant microbes in global oceanic surface waters and play an important role in driving marine biogeochemical cycles. Magroviruses - the viruses of MGII archaea have been recently found to occur ubiquitously in surface ocean. However, their diversity, distribution, and potential ecological functions in coastal zones especially brackish waters are unknown. Here we obtained 234 non-redundant magroviral genomes from brackish surface waters by using homology searches for viral signature proteins highlighting the uncovered vast diversity of this novel viral group. Phylogenetic analysis based on these brackish magroviruses along with previously reported marine ones identified six taxonomic groups with close evolutionary connection to both haloviruses and the viruses of Marine Group I archaea. Magroviruses were present abundantly both in brackish and open ocean samples with some showing habitat specification and others having broad spectrums of distribution between different habitats. Genome annotation suggests they may be involved in regulating multiple metabolic pathways of MGII archaea. Our results uncover the previously overlooked diversity and ecological potentials of a major archaeal virial group in global ocean and brackish waters and shed light on the cryptic evolutionary history of archaeal viruses.
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Affiliation(s)
- Bu Xu
- School of Environment, Harbin Institute of Technology, Harbin, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Lu Fan
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- *Correspondence: Lu Fan,
| | - Wenxiu Wang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Yuanqing Zhu
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai, China
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14
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Heyerhoff B, Engelen B, Bunse C. Auxiliary Metabolic Gene Functions in Pelagic and Benthic Viruses of the Baltic Sea. Front Microbiol 2022; 13:863620. [PMID: 35875520 PMCID: PMC9301287 DOI: 10.3389/fmicb.2022.863620] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 06/02/2022] [Indexed: 11/13/2022] Open
Abstract
Marine microbial communities are facing various ecosystem fluctuations (e.g., temperature, organic matter concentration, salinity, or redox regimes) and thus have to be highly adaptive. This might be supported by the acquisition of auxiliary metabolic genes (AMGs) originating from virus infections. Marine bacteriophages frequently contain AMGs, which allow them to augment their host’s metabolism or enhance virus fitness. These genes encode proteins for the same metabolic functions as their highly similar host homologs. In the present study, we analyzed the diversity, distribution, and composition of marine viruses, focusing on AMGs to identify their putative ecologic role. We analyzed viruses and assemblies of 212 publicly available metagenomes obtained from sediment and water samples across the Baltic Sea. In general, the virus composition in both compartments differed compositionally. While the predominant viral lifestyle was found to be lytic, lysogeny was more prevalent in sediments than in the pelagic samples. The highest proportion of AMGs was identified in the genomes of Myoviridae. Overall, the most abundantly occurring AMGs are encoded for functions that protect viruses from degradation by their hosts, such as methylases. Additionally, some detected AMGs are known to be involved in photosynthesis, 7-cyano-7-deazaguanine synthesis, and cobalamin biosynthesis among other functions. Several AMGs that were identified in this study were previously detected in a large-scale analysis including metagenomes from various origins, i.e., different marine sites, wastewater, and the human gut. This supports the theory of globally conserved core AMGs that are spread over virus genomes, regardless of host or environment.
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15
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Zhao J, Jing H, Wang Z, Wang L, Jian H, Zhang R, Xiao X, Chen F, Jiao N, Zhang Y. Novel Viral Communities Potentially Assisting in Carbon, Nitrogen, and Sulfur Metabolism in the Upper Slope Sediments of Mariana Trench. mSystems 2022; 7:e0135821. [PMID: 35089086 PMCID: PMC8725595 DOI: 10.1128/msystems.01358-21] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/08/2021] [Indexed: 01/12/2023] Open
Abstract
Viruses are ubiquitous in the oceans. Even in the deep sediments of the Mariana Trench, viruses have high productivity. However, little is known about their species composition and survival strategies in that environment. Here, we uncovered novel viral communities (3,206 viral scaffolds) in the upper slope sediments of the Mariana Trench via metagenomic analysis of 15 sediment samples. Most (99%) of the viral scaffolds lack known viral homologs, and ca. 59% of the high-quality viral genomes (total of 111 with completeness of >90%) represent novel genera, including some Phycodnaviridae and jumbo phages. These viruses contain various auxiliary metabolic genes (AMGs) potentially involved in organic carbon degradation, inorganic carbon fixation, denitrification, and assimilatory sulfate reduction, etc. This study provides novel insight into the almost unknown benthic viral communities in the Mariana Trench. IMPORTANCE The Mariana Trench harbors a substantial number of infective viral particles. However, very little is known about the identity, survival strategy, and potential functions of viruses in the trench sediments. Here, through metagenomic analysis, unusual benthic viral communities with high diversity and novelty were discovered. Among them, 59% of the viruses with a genome completeness of >90% represent novel genera. Various auxiliary metabolic genes carried by these viruses reflect the potential adaptive characteristics of viruses in this extreme environment and the biogeochemical cycles that they may participate in. This study gives us a deeper understanding of the peculiarities of viral communities in deep-sea/hadal sediments.
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Affiliation(s)
- Jiulong Zhao
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zengmeng Wang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Long Wang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- State Key Laboratory for Marine Environmental Science, Xiamen University, Xiamen, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Rui Zhang
- State Key Laboratory for Marine Environmental Science, Xiamen University, Xiamen, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Feng Chen
- University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
| | - Nianzhi Jiao
- State Key Laboratory for Marine Environmental Science, Xiamen University, Xiamen, China
| | - Yongyu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
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16
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Aguinaga OE, White KN, Dean AP, Pittman JK. Addition of organic acids to acid mine drainage polluted wetland sediment leads to microbial community structure and functional changes and improved water quality. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 290:118064. [PMID: 34481302 DOI: 10.1016/j.envpol.2021.118064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 06/13/2023]
Abstract
Acid mine drainage (AMD) is a serious environmental problem worldwide that requires efficient and sustainable remediation technologies including the use of biological mechanisms. A key challenge for AMD bioremediation is to provide optimal conditions for microbial-mediated immobilisation of trace metals. Although organic carbon and oxygen can enhance treatment efficiency, the effect on microbial communities is unclear. In this study, surface sediments from a natural wetland with proven efficiency for AMD bioremediation were artificially exposed to oxygen (by aeration) and/or organic carbon (in the form of mixed organic acids) and incubated under laboratory conditions. In addition to measuring changes in water chemistry, a metagenomics approach was used to determine changes in sediment bacterial, archaeal and fungal community structure, and functional gene abundance. The addition of organic carbon produced major changes in the abundance of microorganisms related to iron and sulfur metabolism (including Geobacter and Pelobacter) and increased levels of particulate metals via sulfate reduction. Aeration resulted in an increase in Sideroxydans abundance but no significant changes in metal chemistry were observed. The study concludes that the utilisation of organic carbon by microorganisms is more important for achieving efficient AMD treatment than the availability of oxygen, yet the combination of oxygen with organic carbon addition did not inhibit the improvements to water quality.
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Affiliation(s)
- Oscar E Aguinaga
- Department of Earth and Environmental Sciences, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK; Departamento de Ingeniería, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Keith N White
- Department of Earth and Environmental Sciences, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Andrew P Dean
- Department of Natural Sciences, Faculty of Science and Engineering, Manchester Metropolitan University, Oxford Road, Manchester, M1 5GD, UK
| | - Jon K Pittman
- Department of Earth and Environmental Sciences, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.
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17
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Biosynthesis of Ditropolonyl Sulfide, an Antibacterial Compound Produced by Burkholderia cepacia Complex Strain R-12632. Appl Environ Microbiol 2021; 87:e0116921. [PMID: 34524894 DOI: 10.1128/aem.01169-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Burkholderia cepacia complex strain R-12632 produces ditropolonyl sulfide, an unusual sulfur-containing tropone, via a yet-unknown biosynthetic pathway. Ditropolonyl sulfide purified from a culture of strain R-12632 inhibits the growth of various Gram-positive and Gram-negative resistant bacteria, with MIC values as low as 16 μg/ml. In the present study, we used a transposon mutagenesis approach combined with metabolite analyses to identify the genetic basis for antibacterial activity of strain R-12632 against Gram-negative bacterial pathogens. Fifteen of the 8304 transposon mutants investigated completely lost antibacterial activity against Klebsiella pneumoniae LMG 2095. In these loss-of-activity mutants, nine genes were interrupted. Four of those genes were involved in assimilatory sulfate reduction, two were involved in phenylacetic acid (PAA) catabolism, and one was involved in glutathione metabolism. Via semipreparative fractionation and metabolite identification, it was confirmed that inactivation of the PAA degradation pathway or glutathione metabolism led to loss of ditropolonyl sulfide production. Based on earlier studies on the biosynthesis of tropolone compounds, the requirement for a functional PAA catabolic pathway for antibacterial activity in strain R-12632 indicated that this pathway likely provides the tropolone backbone for ditropolonyl sulfide. Loss of activity observed in mutants defective in assimilatory sulfate reduction and glutathione biosynthesis suggested that cysteine and glutathione are potential sources of the sulfur atom linking the two tropolone moieties. The demonstrated antibacterial activity of the unusual antibacterial compound ditropolonyl sulfide warrants further studies into its biosynthesis and biological role. IMPORTANCE Burkholderia bacteria are historically known for their biocontrol properties and have been proposed as a promising and underexplored source of bioactive specialized metabolites. Burkholderia cepacia complex strain R-12632 inhibits various Gram-positive and Gram-negative resistant pathogens and produces numerous specialized metabolites, among which is ditropolonyl sulfide. This unusual antimicrobial has been poorly studied and its biosynthetic pathway remains unknown. In the present study, we performed transposon mutagenesis of strain R-12632 and performed genome and metabolite analyses of loss-of-activity mutants to study the genetic basis for antibacterial activity. Our results indicate that phenylacetic acid catabolism, assimilatory sulfate reduction, and glutathione metabolism are necessary for ditropolonyl sulfide production. These findings contribute to understanding of the biosynthesis and biological role of this unusual antimicrobial.
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18
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Moya-Beltrán A, Makarova KS, Acuña LG, Wolf YI, Covarrubias PC, Shmakov SA, Silva C, Tolstoy I, Johnson DB, Koonin EV, Quatrini R. Evolution of Type IV CRISPR-Cas Systems: Insights from CRISPR Loci in Integrative Conjugative Elements of Acidithiobacillia. CRISPR J 2021; 4:656-672. [PMID: 34582696 DOI: 10.1089/crispr.2021.0051] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Type IV CRISPR-Cas are a distinct variety of highly derived CRISPR-Cas systems that appear to have evolved from type III systems through the loss of the target-cleaving nuclease and partial deterioration of the large subunit of the effector complex. All known type IV CRISPR-Cas systems are encoded on plasmids, integrative and conjugative elements (ICEs), or prophages, and are thought to contribute to competition between these elements, although the mechanistic details of their function remain unknown. There is a clear parallel between the compositions and likely origin of type IV and type I systems recruited by Tn7-like transposons and mediating RNA-guided transposition. We investigated the diversity and evolutionary relationships of type IV systems, with a focus on those in Acidithiobacillia, where this variety of CRISPR is particularly abundant and always found on ICEs. Our analysis revealed remarkable evolutionary plasticity of type IV CRISPR-Cas systems, with adaptation and ancillary genes originating from different ancestral CRISPR-Cas varieties, and extensive gene shuffling within the type IV loci. The adaptation module and the CRISPR array apparently were lost in the type IV ancestor but were subsequently recaptured by type IV systems on several independent occasions. We demonstrate a high level of heterogeneity among the repeats with type IV CRISPR arrays, which far exceed the heterogeneity of any other known CRISPR repeats and suggest a unique adaptation mechanism. The spacers in the type IV arrays, for which protospacers could be identified, match plasmid genes, in particular those encoding the conjugation apparatus components. Both the biochemical mechanism of type IV CRISPR-Cas function and their role in the competition among mobile genetic elements remain to be investigated.
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Affiliation(s)
- Ana Moya-Beltrán
- Fundación Ciencia y Vida, Santiago, Chile; Universidad San Sebastián, Santiago, Chile.,ANID-Millennium Science Initiative Program, Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile; Universidad San Sebastián, Santiago, Chile
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA; Universidad San Sebastián, Santiago, Chile
| | - Lillian G Acuña
- Fundación Ciencia y Vida, Santiago, Chile; Universidad San Sebastián, Santiago, Chile
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA; Universidad San Sebastián, Santiago, Chile
| | - Paulo C Covarrubias
- Fundación Ciencia y Vida, Santiago, Chile; Universidad San Sebastián, Santiago, Chile
| | - Sergey A Shmakov
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA; Universidad San Sebastián, Santiago, Chile
| | - Cristian Silva
- Fundación Ciencia y Vida, Santiago, Chile; Universidad San Sebastián, Santiago, Chile
| | - Igor Tolstoy
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA; Universidad San Sebastián, Santiago, Chile
| | - D Barrie Johnson
- School of Natural Sciences, Bangor University, Bangor, United Kingdom; Universidad San Sebastián, Santiago, Chile.,Faculty of Health and Life Sciences, Coventry University, Coventry, United Kingdom; and Universidad San Sebastián, Santiago, Chile
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA; Universidad San Sebastián, Santiago, Chile
| | - Raquel Quatrini
- Fundación Ciencia y Vida, Santiago, Chile; Universidad San Sebastián, Santiago, Chile.,ANID-Millennium Science Initiative Program, Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile; Universidad San Sebastián, Santiago, Chile.,Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
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19
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Lauman P, Dennis JJ. Advances in Phage Therapy: Targeting the Burkholderia cepacia Complex. Viruses 2021; 13:1331. [PMID: 34372537 PMCID: PMC8310193 DOI: 10.3390/v13071331] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/29/2021] [Accepted: 07/06/2021] [Indexed: 01/16/2023] Open
Abstract
The increasing prevalence and worldwide distribution of multidrug-resistant bacterial pathogens is an imminent danger to public health and threatens virtually all aspects of modern medicine. Particularly concerning, yet insufficiently addressed, are the members of the Burkholderia cepacia complex (Bcc), a group of at least twenty opportunistic, hospital-transmitted, and notoriously drug-resistant species, which infect and cause morbidity in patients who are immunocompromised and those afflicted with chronic illnesses, including cystic fibrosis (CF) and chronic granulomatous disease (CGD). One potential solution to the antimicrobial resistance crisis is phage therapy-the use of phages for the treatment of bacterial infections. Although phage therapy has a long and somewhat checkered history, an impressive volume of modern research has been amassed in the past decades to show that when applied through specific, scientifically supported treatment strategies, phage therapy is highly efficacious and is a promising avenue against drug-resistant and difficult-to-treat pathogens, such as the Bcc. In this review, we discuss the clinical significance of the Bcc, the advantages of phage therapy, and the theoretical and clinical advancements made in phage therapy in general over the past decades, and apply these concepts specifically to the nascent, but growing and rapidly developing, field of Bcc phage therapy.
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Affiliation(s)
| | - Jonathan J. Dennis
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada;
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20
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Martínez-Ruiz EB, Cooper M, Barrero-Canosa J, Haryono MAS, Bessarab I, Williams RBH, Szewzyk U. Genome analysis of Pseudomonas sp. OF001 and Rubrivivax sp. A210 suggests multicopper oxidases catalyze manganese oxidation required for cylindrospermopsin transformation. BMC Genomics 2021; 22:464. [PMID: 34157973 PMCID: PMC8218464 DOI: 10.1186/s12864-021-07766-0] [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: 10/09/2020] [Accepted: 06/03/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cylindrospermopsin is a highly persistent cyanobacterial secondary metabolite toxic to humans and other living organisms. Strain OF001 and A210 are manganese-oxidizing bacteria (MOB) able to transform cylindrospermopsin during the oxidation of Mn2+. So far, the enzymes involved in manganese oxidation in strain OF001 and A210 are unknown. Therefore, we analyze the genomes of two cylindrospermopsin-transforming MOB, Pseudomonas sp. OF001 and Rubrivivax sp. A210, to identify enzymes that could catalyze the oxidation of Mn2+. We also investigated specific metabolic features related to pollutant degradation and explored the metabolic potential of these two MOB with respect to the role they may play in biotechnological applications and/or in the environment. RESULTS Strain OF001 encodes two multicopper oxidases and one haem peroxidase potentially involved in Mn2+ oxidation, with a high similarity to manganese-oxidizing enzymes described for Pseudomonas putida GB-1 (80, 83 and 42% respectively). Strain A210 encodes one multicopper oxidase potentially involved in Mn2+ oxidation, with a high similarity (59%) to the manganese-oxidizing multicopper oxidase in Leptothrix discophora SS-1. Strain OF001 and A210 have genes that might confer them the ability to remove aromatic compounds via the catechol meta- and ortho-cleavage pathway, respectively. Based on the genomic content, both strains may grow over a wide range of O2 concentrations, including microaerophilic conditions, fix nitrogen, and reduce nitrate and sulfate in an assimilatory fashion. Moreover, the strain A210 encodes genes which may convey the ability to reduce nitrate in a dissimilatory manner, and fix carbon via the Calvin cycle. Both MOB encode CRISPR-Cas systems, several predicted genomic islands, and phage proteins, which likely contribute to their genome plasticity. CONCLUSIONS The genomes of Pseudomonas sp. OF001 and Rubrivivax sp. A210 encode sequences with high similarity to already described MCOs which may catalyze manganese oxidation required for cylindrospermopsin transformation. Furthermore, the analysis of the general metabolism of two MOB strains may contribute to a better understanding of the niches of cylindrospermopsin-removing MOB in natural habitats and their implementation in biotechnological applications to treat water.
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Affiliation(s)
- Erika Berenice Martínez-Ruiz
- Chair of Environmental Microbiology, Technische Universität Berlin, Institute of Environmental Technology, Straße des 17. Juni 135, 10623, Berlin, Germany.
| | - Myriel Cooper
- Chair of Environmental Microbiology, Technische Universität Berlin, Institute of Environmental Technology, Straße des 17. Juni 135, 10623, Berlin, Germany.
| | - Jimena Barrero-Canosa
- Chair of Environmental Microbiology, Technische Universität Berlin, Institute of Environmental Technology, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Mindia A S Haryono
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, 119077, Singapore
| | - Irina Bessarab
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, 119077, Singapore
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, 119077, Singapore
| | - Ulrich Szewzyk
- Chair of Environmental Microbiology, Technische Universität Berlin, Institute of Environmental Technology, Straße des 17. Juni 135, 10623, Berlin, Germany
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21
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Watanabe M, Chiba Y, Hirai MY. Metabolism and Regulatory Functions of O-Acetylserine, S-Adenosylmethionine, Homocysteine, and Serine in Plant Development and Environmental Responses. FRONTIERS IN PLANT SCIENCE 2021; 12:643403. [PMID: 34025692 PMCID: PMC8137854 DOI: 10.3389/fpls.2021.643403] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/17/2021] [Indexed: 05/19/2023]
Abstract
The metabolism of an organism is closely related to both its internal and external environments. Metabolites can act as signal molecules that regulate the functions of genes and proteins, reflecting the status of these environments. This review discusses the metabolism and regulatory functions of O-acetylserine (OAS), S-adenosylmethionine (AdoMet), homocysteine (Hcy), and serine (Ser), which are key metabolites related to sulfur (S)-containing amino acids in plant metabolic networks, in comparison to microbial and animal metabolism. Plants are photosynthetic auxotrophs that have evolved a specific metabolic network different from those in other living organisms. Although amino acids are the building blocks of proteins and common metabolites in all living organisms, their metabolism and regulation in plants have specific features that differ from those in animals and bacteria. In plants, cysteine (Cys), an S-containing amino acid, is synthesized from sulfide and OAS derived from Ser. Methionine (Met), another S-containing amino acid, is also closely related to Ser metabolism because of its thiomethyl moiety. Its S atom is derived from Cys and its methyl group from folates, which are involved in one-carbon metabolism with Ser. One-carbon metabolism is also involved in the biosynthesis of AdoMet, which serves as a methyl donor in the methylation reactions of various biomolecules. Ser is synthesized in three pathways: the phosphorylated pathway found in all organisms and the glycolate and the glycerate pathways, which are specific to plants. Ser metabolism is not only important in Ser supply but also involved in many other functions. Among the metabolites in this network, OAS is known to function as a signal molecule to regulate the expression of OAS gene clusters in response to environmental factors. AdoMet regulates amino acid metabolism at enzymatic and translational levels and regulates gene expression as methyl donor in the DNA and histone methylation or after conversion into bioactive molecules such as polyamine and ethylene. Hcy is involved in Met-AdoMet metabolism and can regulate Ser biosynthesis at an enzymatic level. Ser metabolism is involved in development and stress responses. This review aims to summarize the metabolism and regulatory functions of OAS, AdoMet, Hcy, and Ser and compare the available knowledge for plants with that for animals and bacteria and propose a future perspective on plant research.
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Affiliation(s)
- Mutsumi Watanabe
- Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
| | - Yukako Chiba
- Graduate School of Life Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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22
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Vijayaraj AS, Mohandass C, Joshi D. Microremediation of tannery wastewater by siderophore producing marine bacteria. ENVIRONMENTAL TECHNOLOGY 2020; 41:3619-3632. [PMID: 31070993 DOI: 10.1080/09593330.2019.1615995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 05/02/2019] [Indexed: 06/09/2023]
Abstract
The present study evaluated the microremediation potential of nine siderophore producing marine bacteria for hazardous raw tannery wastewater from common effluent treatment plant (CETP). Most of the pollutants detected in the wastewater were diminished after the bioremediation process. Further, among the three potent isolates selected for aerobic and anaerobic bioremediation study, Marinobacter hydrocarbonoclasticus demonstrated the highest bioremediation aerobically with a reduction in chromium (88%), sulphate (71%), phosphate (68%) and nitrate (57%). Notably, Nitratireductor kimnyeongensis could attack the effluent under both aerobic and anaerobic conditions as substantiated by statistically significant (p < .05) reduction in the pollutants [chromium (85%), sulphate (63%), Chemical Oxygen Demand (COD) (69%), phosphate (76%)]. From the study it is evident that the pollutant load reduction was achieved under both aerobic and anaerobic conditions, however, aerobic environment was more effective in reducing chromium, Biochemical Oxygen Demand (BOD), sulphate, nitrate and phosphate. The bioremediation efficiency was further confirmed by the bioassay experiments with plant and animal models where higher seed germination, greater plant length and biomass, as well as improved survival rate of Artemia nauplii for bioremediated wastewater was observed as compared to the untreated effluent indicating a significant reduction in toxicity. The results for simultaneous removal of multiple-toxicants thus signify effectiveness and ease of using the robust properties of these marine bacterial strains suggesting their potential application for bioremediation. Hence this could pave a promising way for an environment-friendly and economically feasible clean-up strategy for safer disposal of tannery wastewater.
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Affiliation(s)
- A S Vijayaraj
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, India
| | - C Mohandass
- CSIR-National Institute of Oceanography, Regional Centre, Mumbai, India
| | - Devika Joshi
- Academy of Scientific and Innovative Research, CSIR-National Institute of Oceanography, Dona Paula, Goa, India
- The Energy & Resources Institute (TERI), Coastal Ecology and Marine Resources Center, St Cruz, Goa, India
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23
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Effects of pH value on the expression of key iron/sulfur oxidation genes during bioleaching of chalcopyrite on thermophilic condition. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01453-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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24
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Hicks JL, Mullholland CV. Cysteine biosynthesis in Neisseria species. MICROBIOLOGY-SGM 2018; 164:1471-1480. [PMID: 30307392 DOI: 10.1099/mic.0.000728] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The principal mechanism of reducing sulfur into organic compounds is via the synthesis of l-cysteine. Cysteine is used for protein and glutathione synthesis, as well as being the primary sulfur source for a variety of other molecules, such as biotin, coenzyme A, lipoic acid and more. Glutathione and other cysteine derivatives are important for protection against the oxidative stress that pathogenic bacteria such as Neisseria gonorrhoeae and Neisseria meningitidis encounter during infection. With the alarming rise of antibiotic-resistant strains of N. gonorrhoeae, the development of inhibitors for the future treatment of this disease is critical, and targeting cysteine biosynthesis enzymes could be a promising approach for this. Little is known about the transport of sulfate and thiosulfate and subsequent sulfate reduction and incorporation into cysteine in Neisseria species. In this review we investigate cysteine biosynthesis within Neisseria species and examine the differences between species and with other bacteria. Neisseria species exhibit different arrangements of cysteine biosynthesis genes and have slight differences in how they assimilate sulfate and synthesize cysteine, while, most interestingly, N. gonorrhoeae by virtue of a genome deletion, lacks the ability to reduce sulfate to bisulfide for incorporation into cysteine, and as such uses the thiosulfate uptake pathway for the synthesis of cysteine.
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Affiliation(s)
- Joanna L Hicks
- School of Science, University of Waikato, Gate 8 Hillcrest Road, Hamilton, 3216, New Zealand
| | - Claire V Mullholland
- School of Science, University of Waikato, Gate 8 Hillcrest Road, Hamilton, 3216, New Zealand
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25
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Becana M, Wienkoop S, Matamoros MA. Sulfur Transport and Metabolism in Legume Root Nodules. FRONTIERS IN PLANT SCIENCE 2018; 9:1434. [PMID: 30364181 PMCID: PMC6192434 DOI: 10.3389/fpls.2018.01434] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/10/2018] [Indexed: 05/10/2023]
Abstract
Sulfur is an essential nutrient in plants as a constituent element of some amino acids, metal cofactors, coenzymes, and secondary metabolites. Not surprisingly, sulfur deficiency decreases plant growth, photosynthesis, and seed yield in both legumes and non-legumes. In nodulated legumes, sulfur supply is positively linked to symbiotic nitrogen fixation (SNF) and sulfur starvation causes three additional major effects: decrease of nodulation, inhibition of SNF, and slowing down of nodule metabolism. These effects are due, at least in part, to the impairment of nitrogenase biosynthesis and activity, the accumulation of nitrogen-rich amino acids, and the decline in leghemoglobin, ferredoxin, ATP, and glucose in nodules. During the last decade, some major advances have been made about the uptake and metabolism of sulfur in nodules. These include the identification of the sulfate transporter SST1 in the symbiosomal membrane, the finding that glutathione produced in the bacteroids and host cells is essential for nodule activity, and the demonstration that sulfur assimilation in the whole plant is reprogrammed during symbiosis. However, many crucial questions still remain and some examples follow. In the first place, it is of paramount importance to elucidate the mechanism by which sulfur deficiency limits SNF. It is unknown why homoglutahione replaces glutathione as a major water-soluble antioxidant, redox buffer, and sulfur reservoir, among other relevant functions, only in certain legumes and also in different tissues of the same legume species. Much more work is required to identify oxidative post-translational modifications entailing cysteine and methionine residues and to determine how these modifications affect protein function and metabolism in nodules. Likewise, most interactions of antioxidant metabolites and enzymes bearing redox-active sulfur with transcription factors need to be defined. Solving these questions will pave the way to decipher sulfur-dependent mechanisms that regulate SNF, thereby gaining a deep insight into how nodulated legumes adapt to the fluctuating availability of nutrients in the soil.
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Affiliation(s)
- Manuel Becana
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Zaragoza, Spain
| | - Stefanie Wienkoop
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Manuel A. Matamoros
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Zaragoza, Spain
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26
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Faure G, Makarova KS, Koonin EV. CRISPR-Cas: Complex Functional Networks and Multiple Roles beyond Adaptive Immunity. J Mol Biol 2018; 431:3-20. [PMID: 30193985 DOI: 10.1016/j.jmb.2018.08.030] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 08/28/2018] [Accepted: 08/29/2018] [Indexed: 01/26/2023]
Abstract
CRISPR-Cas is a prokaryotic adaptive immune system that functions by incorporating fragments of foreign DNA into CRISPR arrays. The arrays containing spacers derived from foreign DNA are transcribed, and the transcripts are processed to generate spacer-containing mature CRISPR-RNAs that are employed as guides to specifically recognize and cleave the DNA or RNA of the cognate parasitic genetic elements. The CRISPR-Cas systems show remarkable complexity and diversity of molecular organization and appear to be involved in various cellular functions that are distinct from, even if connected to, adaptive immunity. In this review, we discuss some of such functional links of CRISPR-Cas systems including their effect on horizontal gene transfer that can be either inhibitory or stimulatory, connections between CRISPR-Cas and DNA repair systems as well as programmed cell death and signal transduction mechanisms, and potential role of CRISPR-Cas in transposon integration and plasmid maintenance. The interplay between the primary function of CRISPR-Cas as an adaptive immunity mechanism and these other roles defines the richness of the biological effects of these systems and affects their spread among bacteria and archaea.
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Affiliation(s)
- Guilhem Faure
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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27
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Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis. Proc Natl Acad Sci U S A 2018; 115:E5307-E5316. [PMID: 29784811 DOI: 10.1073/pnas.1803440115] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The CRISPR-Cas systems of bacterial and archaeal adaptive immunity consist of direct repeat arrays separated by unique spacers and multiple CRISPR-associated (cas) genes encoding proteins that mediate all stages of the CRISPR response. In addition to the relatively small set of core cas genes that are typically present in all CRISPR-Cas systems of a given (sub)type and are essential for the defense function, numerous genes occur in CRISPR-cas loci only sporadically. Some of these have been shown to perform various ancillary roles in CRISPR response, but the functional relevance of most remains unknown. We developed a computational strategy for systematically detecting genes that are likely to be functionally linked to CRISPR-Cas. The approach is based on a "CRISPRicity" metric that measures the strength of CRISPR association for all protein-coding genes from sequenced bacterial and archaeal genomes. Uncharacterized genes with CRISPRicity values comparable to those of cas genes are considered candidate CRISPR-linked genes. We describe additional criteria to predict functionally relevance for genes in the candidate set and identify 79 genes as strong candidates for functional association with CRISPR-Cas systems. A substantial majority of these CRISPR-linked genes reside in type III CRISPR-cas loci, which implies exceptional functional versatility of type III systems. Numerous candidate CRISPR-linked genes encode integral membrane proteins suggestive of tight membrane association of CRISPR-Cas systems, whereas many others encode proteins implicated in various signal transduction pathways. These predictions provide ample material for improving annotation of CRISPR-cas loci and experimental characterization of previously unsuspected aspects of CRISPR-Cas system functionality.
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28
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Scott KM, Williams J, Porter CMB, Russel S, Harmer TL, Paul JH, Antonen KM, Bridges MK, Camper GJ, Campla CK, Casella LG, Chase E, Conrad JW, Cruz MC, Dunlap DS, Duran L, Fahsbender EM, Goldsmith DB, Keeley RF, Kondoff MR, Kussy BI, Lane MK, Lawler S, Leigh BA, Lewis C, Lostal LM, Marking D, Mancera PA, McClenthan EC, McIntyre EA, Mine JA, Modi S, Moore BD, Morgan WA, Nelson KM, Nguyen KN, Ogburn N, Parrino DG, Pedapudi AD, Pelham RP, Preece AM, Rampersad EA, Richardson JC, Rodgers CM, Schaffer BL, Sheridan NE, Solone MR, Staley ZR, Tabuchi M, Waide RJ, Wanjugi PW, Young S, Clum A, Daum C, Huntemann M, Ivanova N, Kyrpides N, Mikhailova N, Palaniappan K, Pillay M, Reddy TBK, Shapiro N, Stamatis D, Varghese N, Woyke T, Boden R, Freyermuth SK, Kerfeld CA. Genomes of ubiquitous marine and hypersaline Hydrogenovibrio, Thiomicrorhabdus and Thiomicrospira spp. encode a diversity of mechanisms to sustain chemolithoautotrophy in heterogeneous environments. Environ Microbiol 2018. [PMID: 29521452 DOI: 10.1111/1462-2920.14090] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chemolithoautotrophic bacteria from the genera Hydrogenovibrio, Thiomicrorhabdus and Thiomicrospira are common, sometimes dominant, isolates from sulfidic habitats including hydrothermal vents, soda and salt lakes and marine sediments. Their genome sequences confirm their membership in a deeply branching clade of the Gammaproteobacteria. Several adaptations to heterogeneous habitats are apparent. Their genomes include large numbers of genes for sensing and responding to their environment (EAL- and GGDEF-domain proteins and methyl-accepting chemotaxis proteins) despite their small sizes (2.1-3.1 Mbp). An array of sulfur-oxidizing complexes are encoded, likely to facilitate these organisms' use of multiple forms of reduced sulfur as electron donors. Hydrogenase genes are present in some taxa, including group 1d and 2b hydrogenases in Hydrogenovibrio marinus and H. thermophilus MA2-6, acquired via horizontal gene transfer. In addition to high-affinity cbb3 cytochrome c oxidase, some also encode cytochrome bd-type quinol oxidase or ba3 -type cytochrome c oxidase, which could facilitate growth under different oxygen tensions, or maintain redox balance. Carboxysome operons are present in most, with genes downstream encoding transporters from four evolutionarily distinct families, which may act with the carboxysomes to form CO2 concentrating mechanisms. These adaptations to habitat variability likely contribute to the cosmopolitan distribution of these organisms.
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Affiliation(s)
- Kathleen M Scott
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - John Williams
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Cody M B Porter
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Sydney Russel
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Tara L Harmer
- Biology Program, Stockton University, Galloway, NJ, USA
| | - John H Paul
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Kirsten M Antonen
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Megan K Bridges
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Gary J Camper
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Christie K Campla
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Leila G Casella
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Eva Chase
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - James W Conrad
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Mercedez C Cruz
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Darren S Dunlap
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Laura Duran
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Elizabeth M Fahsbender
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Dawn B Goldsmith
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Ryan F Keeley
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Matthew R Kondoff
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Breanna I Kussy
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Marannda K Lane
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Stephanie Lawler
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Brittany A Leigh
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Courtney Lewis
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Lygia M Lostal
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Devon Marking
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Paola A Mancera
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Evan C McClenthan
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Emily A McIntyre
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Jessica A Mine
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Swapnil Modi
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Brittney D Moore
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - William A Morgan
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Kaleigh M Nelson
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Kimmy N Nguyen
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Nicholas Ogburn
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - David G Parrino
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Anangamanjari D Pedapudi
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Rebecca P Pelham
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Amanda M Preece
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Elizabeth A Rampersad
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Jason C Richardson
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Christina M Rodgers
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Brent L Schaffer
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Nancy E Sheridan
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Michael R Solone
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Zachery R Staley
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Maki Tabuchi
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Ramond J Waide
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Pauline W Wanjugi
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Suzanne Young
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Alicia Clum
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Chris Daum
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Marcel Huntemann
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Nikos Kyrpides
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | | | | | - Manoj Pillay
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - T B K Reddy
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Nicole Shapiro
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Neha Varghese
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Rich Boden
- School of Biological & Marine Sciences, University of Plymouth, Drake Circus, Plymouth, UK.,Sustainable Earth Institute, University of Plymouth, Drake Circus, Plymouth, UK
| | | | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.,MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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29
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Becana M, Wienkoop S, Matamoros MA. Sulfur Transport and Metabolism in Legume Root Nodules. FRONTIERS IN PLANT SCIENCE 2018. [PMID: 30364181 DOI: 10.3389/fpls.2018:01434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Sulfur is an essential nutrient in plants as a constituent element of some amino acids, metal cofactors, coenzymes, and secondary metabolites. Not surprisingly, sulfur deficiency decreases plant growth, photosynthesis, and seed yield in both legumes and non-legumes. In nodulated legumes, sulfur supply is positively linked to symbiotic nitrogen fixation (SNF) and sulfur starvation causes three additional major effects: decrease of nodulation, inhibition of SNF, and slowing down of nodule metabolism. These effects are due, at least in part, to the impairment of nitrogenase biosynthesis and activity, the accumulation of nitrogen-rich amino acids, and the decline in leghemoglobin, ferredoxin, ATP, and glucose in nodules. During the last decade, some major advances have been made about the uptake and metabolism of sulfur in nodules. These include the identification of the sulfate transporter SST1 in the symbiosomal membrane, the finding that glutathione produced in the bacteroids and host cells is essential for nodule activity, and the demonstration that sulfur assimilation in the whole plant is reprogrammed during symbiosis. However, many crucial questions still remain and some examples follow. In the first place, it is of paramount importance to elucidate the mechanism by which sulfur deficiency limits SNF. It is unknown why homoglutahione replaces glutathione as a major water-soluble antioxidant, redox buffer, and sulfur reservoir, among other relevant functions, only in certain legumes and also in different tissues of the same legume species. Much more work is required to identify oxidative post-translational modifications entailing cysteine and methionine residues and to determine how these modifications affect protein function and metabolism in nodules. Likewise, most interactions of antioxidant metabolites and enzymes bearing redox-active sulfur with transcription factors need to be defined. Solving these questions will pave the way to decipher sulfur-dependent mechanisms that regulate SNF, thereby gaining a deep insight into how nodulated legumes adapt to the fluctuating availability of nutrients in the soil.
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Affiliation(s)
- Manuel Becana
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Zaragoza, Spain
| | - Stefanie Wienkoop
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Manuel A Matamoros
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Zaragoza, Spain
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Paritala H, Palde PB, Carroll KS. Functional Site Discovery in a Sulfur Metabolism Enzyme by Using Directed Evolution. Chembiochem 2016; 17:1873-1878. [PMID: 27411165 DOI: 10.1002/cbic.201600264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Indexed: 11/07/2022]
Abstract
In human pathogens, the sulfate assimilation pathway provides reduced sulfur for biosynthesis of essential metabolites, including cysteine and low-molecular-weight thiol compounds. Sulfonucleotide reductases (SRs) catalyze the first committed step of sulfate reduction. In this reaction, activated sulfate in the form of adenosine-5'-phosphosulfate (APS) or 3'-phosphoadenosine 5'-phosphosulfate (PAPS) is reduced to sulfite. Gene knockout, transcriptomic and proteomic data have established the importance of SRs in oxidative stress-inducible antimicrobial resistance mechanisms. In previous work, we focused on rational and high-throughput design of small-molecule inhibitors that target the active site of SRs. However, another critical goal is to discover functionally important regions in SRs beyond the traditional active site. As an alternative to conservation analysis, we used directed evolution to rapidly identify functional sites in PAPS reductase (PAPR). Four new regions were discovered that are essential to PAPR function and lie outside the substrate binding pocket. Our results highlight the use of directed evolution as a tool to rapidly discover functionally important sites in proteins.
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Affiliation(s)
- Hanumantharao Paritala
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, 2B2, Jupiter, FL, 33458, USA
| | - Prakash B Palde
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, 2B2, Jupiter, FL, 33458, USA
| | - Kate S Carroll
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, 2B2, Jupiter, FL, 33458, USA.
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Koprivova A, Kopriva S. Sulfation pathways in plants. Chem Biol Interact 2016; 259:23-30. [PMID: 27206694 DOI: 10.1016/j.cbi.2016.05.021] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/02/2016] [Accepted: 05/16/2016] [Indexed: 11/27/2022]
Abstract
Plants take up sulfur in the form of sulfate. Sulfate is activated to adenosine 5'-phosphosulfate (APS) and reduced to sulfite and then to sulfide when it is assimilated into amino acid cysteine. Alternatively, APS is phosphorylated to 3'-phosphoadenosine 5'-phosphosulfate (PAPS), and sulfate from PAPS is transferred onto diverse metabolites in its oxidized form. Traditionally, these pathways are referred to as primary and secondary sulfate metabolism, respectively. However, the synthesis of PAPS is essential for plants and even its reduced provision leads to dwarfism. Here the current knowledge of enzymes involved in sulfation pathways of plants will be summarized, the similarities and differences between different kingdoms will be highlighted, and major open questions in the research of plant sulfation will be formulated.
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Affiliation(s)
- Anna Koprivova
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany.
| | - Stanislav Kopriva
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany.
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Jacob JM, Lens PNL, Balakrishnan RM. Microbial synthesis of chalcogenide semiconductor nanoparticles: a review. Microb Biotechnol 2016; 9:11-21. [PMID: 26110980 PMCID: PMC4720408 DOI: 10.1111/1751-7915.12297] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 05/04/2015] [Accepted: 05/09/2015] [Indexed: 02/02/2023] Open
Abstract
Chalcogenide semiconductor quantum dots are emerging as promising nanomaterials due to their size tunable optoelectronic properties. The commercial synthesis and their subsequent integration for practical uses have, however, been contorted largely due to the toxicity and cost issues associated with the present chemical synthesis protocols. Accordingly, there is an immediate need to develop alternative environment-friendly synthesis procedures. Microbial factories hold immense potential to achieve this objective. Over the past few years, bacteria, fungi and yeasts have been experimented with as eco-friendly and cost-effective tools for the biosynthesis of semiconductor quantum dots. This review provides a detailed overview about the production of chalcogen-based semiconductor quantum particles using the inherent microbial machinery.
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Affiliation(s)
- Jaya Mary Jacob
- Department of Chemical Engineering, National Institute of Technology Karnataka, Surathkal, Mangalore, Karnataka, 575 025, India
| | - Piet N L Lens
- UNESCO-IHE Institute for Water Education, Delft, Netherlands
| | - Raj Mohan Balakrishnan
- Department of Chemical Engineering, National Institute of Technology Karnataka, Surathkal, Mangalore, Karnataka, 575 025, India
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Zhu XM, Hackl S, Thaker MN, Kalan L, Weber C, Urgast DS, Krupp EM, Brewer A, Vanner S, Szawiola A, Yim G, Feldmann J, Bechthold A, Wright GD, Zechel DL. Biosynthesis of the Fluorinated Natural Product Nucleocidin inStreptomyces calvusIs Dependent on thebldA-Specified Leu-tRNAUUAMolecule. Chembiochem 2015; 16:2498-506. [DOI: 10.1002/cbic.201500402] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Xi Ming Zhu
- Department of Chemistry; Queen's University; Chernoff Hall 90 Bader Lane Kingston Ontario K7L 3N6 Canada
| | - Stefanie Hackl
- Department of Pharmaceutical Biology and Biotechnology; Institute of Pharmaceutical Sciences; Albert-Ludwigs-Universität Freiburg; Stefan-Meier-Strasse 19 79104 Freiburg Germany
| | - Maulik N. Thaker
- Michael G. DeGroote Institute for Infectious Disease Research; McMaster University; 1200 Main Street West Hamilton Ontario L8N 3Z5 Canada
| | - Lindsay Kalan
- Michael G. DeGroote Institute for Infectious Disease Research; McMaster University; 1200 Main Street West Hamilton Ontario L8N 3Z5 Canada
| | - Claudia Weber
- Trace Element Speciation Laboratory; Department of Chemistry; University of Aberdeen; Aberdeen AB24 3UE UK
| | - Dagmar S. Urgast
- Trace Element Speciation Laboratory; Department of Chemistry; University of Aberdeen; Aberdeen AB24 3UE UK
| | - Eva M. Krupp
- Trace Element Speciation Laboratory; Department of Chemistry; University of Aberdeen; Aberdeen AB24 3UE UK
| | - Alyssa Brewer
- Department of Chemistry; Queen's University; Chernoff Hall 90 Bader Lane Kingston Ontario K7L 3N6 Canada
| | - Stephanie Vanner
- Department of Chemistry; Queen's University; Chernoff Hall 90 Bader Lane Kingston Ontario K7L 3N6 Canada
| | - Anjuli Szawiola
- Department of Chemistry; Queen's University; Chernoff Hall 90 Bader Lane Kingston Ontario K7L 3N6 Canada
| | - Grace Yim
- Michael G. DeGroote Institute for Infectious Disease Research; McMaster University; 1200 Main Street West Hamilton Ontario L8N 3Z5 Canada
| | - Jörg Feldmann
- Trace Element Speciation Laboratory; Department of Chemistry; University of Aberdeen; Aberdeen AB24 3UE UK
| | - Andreas Bechthold
- Department of Pharmaceutical Biology and Biotechnology; Institute of Pharmaceutical Sciences; Albert-Ludwigs-Universität Freiburg; Stefan-Meier-Strasse 19 79104 Freiburg Germany
| | - Gerard D. Wright
- Michael G. DeGroote Institute for Infectious Disease Research; McMaster University; 1200 Main Street West Hamilton Ontario L8N 3Z5 Canada
| | - David L. Zechel
- Department of Chemistry; Queen's University; Chernoff Hall 90 Bader Lane Kingston Ontario K7L 3N6 Canada
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Expression of Critical Sulfur- and Iron-Oxidation Genes and the Community Dynamics During Bioleaching of Chalcopyrite Concentrate by Moderate Thermophiles. Curr Microbiol 2015; 71:62-9. [DOI: 10.1007/s00284-015-0817-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 03/05/2015] [Indexed: 10/23/2022]
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CysB Negatively Affects the Transcription of pqsR and Pseudomonas Quinolone Signal Production in Pseudomonas aeruginosa. J Bacteriol 2015; 197:1988-2002. [PMID: 25845844 DOI: 10.1128/jb.00246-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 03/27/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Pseudomonas aeruginosa is a Gram-negative bacterium that is ubiquitous in the environment, and it is an opportunistic pathogen that can infect a variety of hosts, including humans. During the process of infection, P. aeruginosa coordinates the expression of numerous virulence factors through the production of multiple cell-to-cell signaling molecules. The production of these signaling molecules is linked through a regulatory network, with the signal N-(3-oxododecanoyl) homoserine lactone and its receptor LasR controlling the induction of a second acyl-homoserine lactone signal and the Pseudomonas quinolone signal (PQS). LasR-mediated control of PQS occurs partly by activating the transcription of pqsR, a gene that encodes the PQS receptor and is necessary for PQS production. We show that LasR interacts with a single binding site in the pqsR promoter region and that it does not influence the transcription of the divergently transcribed gene, nadA. Using DNA affinity chromatography, we identified additional proteins that interact with the pqsR-nadA intergenic region. These include the H-NS family members MvaT and MvaU, and CysB, a transcriptional regulator that controls sulfur uptake and cysteine biosynthesis. We show that CysB interacts with the pqsR promoter and that CysB represses pqsR transcription and PQS production. Additionally, we provide evidence that CysB can interfere with the activation of pqsR transcription by LasR. However, as seen with other CysB-regulated genes, pqsR expression was not differentially regulated in response to cysteine levels. These findings demonstrate a novel role for CysB in influencing cell-to-cell signal production by P. aeruginosa. IMPORTANCE The production of PQS and other 4-hydroxy-2-alkylquinolone (HAQs) compounds is a key component of the P. aeruginosa cell-to-cell signaling network, impacts multiple physiological functions, and is required for virulence. PqsR directly regulates the genes necessary for HAQ production, but little is known about the regulation of pqsR. We identified CysB as a novel regulator of pqsR and PQS production, but, unlike other CysB-controlled genes, it does not appear to regulate pqsR in response to cysteine. This implies that CysB functions as both a cysteine-responsive and cysteine-unresponsive regulator in P. aeruginosa.
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Justice NB, Norman A, Brown CT, Singh A, Thomas BC, Banfield JF. Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms. BMC Genomics 2014; 15:1107. [PMID: 25511286 PMCID: PMC4378227 DOI: 10.1186/1471-2164-15-1107] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 11/27/2014] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Bacteria of the genus Sulfobacillus are found worldwide as members of microbial communities that accelerate sulfide mineral dissolution in acid mine drainage environments (AMD), acid-rock drainage environments (ARD), as well as in industrial bioleaching operations. Despite their frequent identification in these environments, their role in biogeochemical cycling is poorly understood. RESULTS Here we report draft genomes of five species of the Sulfobacillus genus (AMDSBA1-5) reconstructed by cultivation-independent sequencing of biofilms sampled from the Richmond Mine (Iron Mountain, CA). Three of these species (AMDSBA2, AMDSBA3, and AMDSBA4) have no cultured representatives while AMDSBA1 is a strain of S. benefaciens, and AMDSBA5 a strain of S. thermosulfidooxidans. We analyzed the diversity of energy conservation and central carbon metabolisms for these genomes and previously published Sulfobacillus genomes. Pathways of sulfur oxidation vary considerably across the genus, including the number and type of subunits of putative heterodisulfide reductase complexes likely involved in sulfur oxidation. The number and type of nickel-iron hydrogenase proteins varied across the genus, as does the presence of different central carbon pathways. Only the AMDSBA3 genome encodes a dissimilatory nitrate reducatase and only the AMDSBA5 and S. thermosulfidooxidans genomes encode assimilatory nitrate reductases. Within the genus, AMDSBA4 is unusual in that its electron transport chain includes a cytochrome bc type complex, a unique cytochrome c oxidase, and two distinct succinate dehydrogenase complexes. CONCLUSIONS Overall, the results significantly expand our understanding of carbon, sulfur, nitrogen, and hydrogen metabolism within the Sulfobacillus genus.
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Affiliation(s)
- Nicholas B Justice
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
- />Physical Biosciences Division, Lawrence Berkeley National Lab, Berkeley, CA USA
| | - Anders Norman
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
- />Section for Infection Microbiology, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Christopher T Brown
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
| | - Andrea Singh
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
| | - Brian C Thomas
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
| | - Jillian F Banfield
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
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Xiang X, Pan G, Rong T, Zheng ZL, Leustek T. A luciferase-based method for assay of 5'-adenylylsulfate reductase. Anal Biochem 2014; 460:22-8. [PMID: 24857786 DOI: 10.1016/j.ab.2014.05.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 05/13/2014] [Accepted: 05/14/2014] [Indexed: 01/13/2023]
Abstract
A luciferase-based method was developed for measurement of 5'-adenylylsulfate (APS) reductase (APR), an enzyme of the reductive sulfate assimilation pathway in prokaryotes and plants. APR catalyzes the two-electron reduction of APS and forms sulfite and adenosine 5'-monophospahate (AMP). The luciferase-based assay measures AMP production using an enzyme-coupled system that generates luminescence. The method is shown to provide an accurate measurement of APR kinetic properties and can be used for both endpoint and continuous assays. APR activity can be measured from pure enzyme preparations as well as from crude protein extracts of tissues. In addition, the assay is ideally suited to high-throughput sample analysis of APR activity in a microtiter dish format. The method adds new capability to the study of the biochemistry and physiology of APR.
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Affiliation(s)
- Xiaoli Xiang
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ 08901, USA; Institute of Maize Research, Key Laboratory of Biology and Genetic Improvement of Maize in the Southwest Region, Ministry of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Guangtang Pan
- Institute of Maize Research, Key Laboratory of Biology and Genetic Improvement of Maize in the Southwest Region, Ministry of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Tingzhao Rong
- Institute of Maize Research, Key Laboratory of Biology and Genetic Improvement of Maize in the Southwest Region, Ministry of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhi-Liang Zheng
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, NY 10468, USA
| | - Thomas Leustek
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ 08901, USA.
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Wübbeler JH, Hiessl S, Schuldes J, Thürmer A, Daniel R, Steinbüchel A. Unravelling the complete genome sequence of Advenella mimigardefordensis strain DPN7T and novel insights in the catabolism of the xenobiotic polythioester precursor 3,3'-dithiodipropionate. MICROBIOLOGY-SGM 2014; 160:1401-1416. [PMID: 24739217 DOI: 10.1099/mic.0.078279-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Advenella mimigardefordensis strain DPN7(T) is a remarkable betaproteobacterium because of its extraordinary ability to use the synthetic disulfide 3,3'-dithiodipropionic acid (DTDP) as the sole carbon source and electron donor for aerobic growth. One application of DTDP is as a precursor substrate for biotechnically synthesized polythioesters (PTEs), which are interesting non-degradable biopolymers applicable for plastics materials. Metabolic engineering for optimization of PTE production requires an understanding of DTDP conversion. The genome of A. mimigardefordensis strain DPN7(T) was sequenced and annotated. The circular chromosome was found to be composed of 4,740,516 bp and 4112 predicted ORFs, whereas the circular plasmid consisted of 23,610 bp and 24 predicted ORFs. The genes participating in DTDP catabolism had been characterized in detail previously, but knowing the complete genome sequence and with support of Tn5: :mob-induced mutants, putatively involved transporter proteins and a transcriptional regulator were also identified. Most probably, DTDP is transported into the cell by a specific tripartite tricarboxylate transport system and is then cleaved by the disulfide reductase LpdA, sulfoxygenated by the 3-mercaptopropionate dioxygenase Mdo, activated by the CoA ligase SucCD and desulfinated by the acyl-CoA dehydrogenase-like desulfinase AcdA. Regulation of this pathway is presumably performed by a transcriptional regulator of the xenobiotic response element family. The excessive sulfate that is inevitably produced is secreted by the cells by a unique sulfate exporter of the CPA (cation : proton antiporter) superfamily.
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Affiliation(s)
- Jan Hendrik Wübbeler
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Sebastian Hiessl
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Jörg Schuldes
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Andrea Thürmer
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Alexander Steinbüchel
- Faculty of Biology, King Abdulaziz University, Jeddah, Saudi Arabia.,Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
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Biosynthesis and Antimicrobial Activity of Semiconductor Nanoparticles against Oral Pathogens. Bioinorg Chem Appl 2014; 2014:347167. [PMID: 24860280 PMCID: PMC4016845 DOI: 10.1155/2014/347167] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Accepted: 01/10/2014] [Indexed: 11/18/2022] Open
Abstract
Dental care is an essential phenomenon in human health. Oral pathogens can cause severe break which may show the way to serious issues in human disease like blood circulation and coronary disease. In the current study, we demonstrated the synthesis and antimicrobial activity of cadmium sulphide and zinc sulphide nanoparticles against oral pathogens. The process for the synthesis of cadmium sulphide (CdS) and zinc sulphide (ZnS) nanoparticles is fast, novel, and ecofriendly. Formation of cadmium sulphide (CdS) and zinc sulphide (ZnS) nanoparticles was confirmed by surface plasmon spectra using UV-Vis spectrophotometer. The morphology of crystalline phase of nanoparticles was determined from transmission electron microscopy (TEM) and X-ray diffraction (XRD) spectra. The average size of cadmium sulphide (CdS) and zinc sulphide (ZnS) nanoparticles was in the range of 10 nm to 25 nm and 65 nm, respectively, and the observed morphology was spherical. The results indicated that the proteins, which contain amine groups, played a reducing and controlling responsibility during the formation of cadmium sulphide (CdS) and zinc sulphide (ZnS) nanoparticles in the colloidal solution. The antimicrobial activity was assessed against oral pathogens such as Streptococcus sp. Staphylococcus sp. Lactobacillus sp., and Candida albicans and these results confirmed that the sulphide nanoparticles are exhibiting good bactericidal activity.
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Co-expression of bacterial aspartate kinase and adenylylsulfate reductase genes substantially increases sulfur amino acid levels in transgenic alfalfa (Medicago sativa L.). PLoS One 2014; 9:e88310. [PMID: 24520364 PMCID: PMC3919742 DOI: 10.1371/journal.pone.0088310] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 01/07/2014] [Indexed: 11/19/2022] Open
Abstract
Alfalfa (Medicago sativa L.) is one of the most important forage crops used to feed livestock, such as cattle and sheep, and the sulfur amino acid (SAA) content of alfalfa is used as an index of its nutritional value. Aspartate kinase (AK) catalyzes the phosphorylation of aspartate to Asp-phosphate, the first step in the aspartate family biosynthesis pathway, and adenylylsulfate reductase (APR) catalyzes the conversion of activated sulfate to sulfite, providing reduced sulfur for the synthesis of cysteine, methionine, and other essential metabolites and secondary compounds. To reduce the feedback inhibition of other metabolites, we cloned bacterial AK and APR genes, modified AK, and introduced them into alfalfa. Compared to the wild-type alfalfa, the content of cysteine increased by 30% and that of methionine increased substantially by 60%. In addition, a substantial increase in the abundance of essential amino acids (EAAs), such as aspartate and lysine, was found. The results also indicated a close connection between amino acid metabolism and the tricarboxylic acid (TCA) cycle. The total amino acid content and the forage biomass tested showed no significant changes in the transgenic plants. This approach provides a new method for increasing SAAs and allows for the development of new genetically modified crops with enhanced nutritional value.
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Stevenson CEM, Hughes RK, McManus MT, Lawson DM, Kopriva S. The X-ray crystal structure of APR-B, an atypical adenosine 5'-phosphosulfate reductase from Physcomitrella patens. FEBS Lett 2013; 587:3626-32. [PMID: 24100135 DOI: 10.1016/j.febslet.2013.09.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 09/03/2013] [Accepted: 09/05/2013] [Indexed: 01/18/2023]
Abstract
Sulfonucleotide reductases catalyse the first reductive step of sulfate assimilation. Their substrate specificities generally correlate with the requirement for a [Fe4S4] cluster, where adenosine 5'-phosphosulfate (APS) reductases possess a cluster and 3'-phosphoadenosine 5'-phosphosulfate reductases do not. The exception is the APR-B isoform of APS reductase from the moss Physcomitrella patens, which lacks a cluster. The crystal structure of APR-B, the first for a plant sulfonucleotide reductase, is consistent with a preference for APS. Structural conservation with bacterial APS reductase rules out a structural role for the cluster, but supports the contention that it enhances the activity of conventional APS reductases.
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Affiliation(s)
- Clare E M Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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Role for ferredoxin:NAD(P)H oxidoreductase (FprA) in sulfate assimilation and siderophore biosynthesis in Pseudomonads. J Bacteriol 2013; 195:3876-87. [PMID: 23794620 DOI: 10.1128/jb.00528-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pyridine-2,6-bis(thiocarboxylate) (PDTC), produced by certain pseudomonads, is a sulfur-containing siderophore that binds iron, as well as a wide range of transition metals, and it affects the net hydrolysis of the environmental contaminant carbon tetrachloride. The pathway of PDTC biosynthesis has not been defined. Here, we performed a transposon screen of Pseudomonas putida DSM 3601 to identify genes necessary for PDTC production (Pdt phenotype). Transposon insertions within genes for sulfate assimilation (cysD, cysNC, and cysG [cobA2]) dominated the collection of Pdt mutations. In addition, two insertions were within the gene for the LysR-type transcriptional activator FinR (PP1637). Phenotypic characterization indicated that finR mutants were cysteine bradytrophs. The Pdt phenotype of finR mutants could be complemented by the known target of FinR regulation, fprA (encoding ferredoxin:NADP(+) oxidoreductase), or by Escherichia coli cysJI (encoding sulfite reductase). These data indicate that fprA is necessary for effective sulfate assimilation by P. putida and that the effect of finR mutation on PDTC production was due to deficient expression of fprA and sulfite reduction. fprA expression in both P. putida and P. aeruginosa was found to be regulated by FinR, but in a manner dependent upon reduced sulfur sources, implicating FinR in sulfur regulatory physiology. The genes and phenotypes identified in this study indicated a strong dependence upon intracellular reduced sulfur/cysteine for PDTC biosynthesis and that pseudomonads utilize sulfite reduction enzymology distinct from that of E. coli and possibly similar to that of chloroplasts and other proteobacteria.
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Zhang M, Ravilious GE, Hicks LM, Jez JM, McCulla RD. Redox Switching of Adenosine-5′-phosphosulfate Kinase with Photoactivatable Atomic Oxygen Precursors. J Am Chem Soc 2012; 134:16979-82. [DOI: 10.1021/ja3078522] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
| | - Geoffrey E. Ravilious
- Department of Biology, Washington University, One Brookings Drive, Campus
Box 1137, Saint Louis, Missouri 63130, United States
| | - Leslie M. Hicks
- Donald Danforth Plant Science Center, 975 North Warson Road, Saint Louis,
Missouri 63132, United States
| | - Joseph M. Jez
- Department of Biology, Washington University, One Brookings Drive, Campus
Box 1137, Saint Louis, Missouri 63130, United States
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Jaramillo ML, Abanto M, Quispe RL, Calderón J, del Valle LJ, Talledo M, Ramírez P. Cloning, expression and bioinformatics analysis of ATP sulfurylase from Acidithiobacillus ferrooxidans ATCC 23270 in Escherichia coli. Bioinformation 2012; 8:695-704. [PMID: 23055613 PMCID: PMC3449377 DOI: 10.6026/97320630008695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 07/11/2012] [Indexed: 11/23/2022] Open
Abstract
Molecular studies of enzymes involved in sulfite oxidation in Acidithiobacillus ferrooxidans have not yet been developed, especially in the ATP sulfurylase (ATPS) of these acidophilus tiobacilli that have importance in biomining. This enzyme synthesizes ATP and sulfate from adenosine phosphosulfate (APS) and pyrophosphate (PPi), final stage of the sulfite oxidation by these organisms in order to obtain energy. The atpS gene (1674 bp) encoding the ATPS from Acidithiobacillus ferrooxidans ATCC 23270 was amplified using PCR, cloned in the pET101-TOPO plasmid, sequenced and expressed in Escherichia coli obtaining a 63.5 kDa ATPS recombinant protein according to SDS-PAGE analysis. The bioinformatics and phylogenetic analyses determined that the ATPS from A. ferrooxidans presents ATP sulfurylase (ATS) and APS kinase (ASK) domains similar to ATPS of Aquifex aeolicus, probably of a more ancestral origin. Enzyme activity towards ATP formation was determined by quantification of ATP formed from E. coli cell extracts, using a bioluminescence assay based on light emission by the luciferase enzyme. Our results demonstrate that the recombinant ATP sulfurylase from A. ferrooxidans presents an enzymatic activity for the formation of ATP and sulfate, and possibly is a bifunctional enzyme due to its high homology to the ASK domain from A. aeolicus and true kinases.
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Affiliation(s)
- Michael L Jaramillo
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima – Peru
| | - Michel Abanto
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima – Peru
| | - Ruth L Quispe
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima – Peru
| | - Julio Calderón
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima – Peru
| | - Luís J del Valle
- Centre díEnginyeria Biotecnologica i Molecular (CEBIM), Departament díEnginyeria Química, ETSEIB, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Miguel Talledo
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima – Peru
| | - Pablo Ramírez
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima – Peru
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Ravilious GE, Jez JM. Structural biology of plant sulfur metabolism: From assimilation to biosynthesis. Nat Prod Rep 2012; 29:1138-52. [DOI: 10.1039/c2np20009k] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Structural basis and evolution of redox regulation in plant adenosine-5'-phosphosulfate kinase. Proc Natl Acad Sci U S A 2011; 109:309-14. [PMID: 22184237 DOI: 10.1073/pnas.1115772108] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Adenosine-5'-phosphosulfate (APS) kinase (APSK) catalyzes the phosphorylation of APS to 3'-phospho-APS (PAPS). In Arabidopsis thaliana, APSK is essential for reproductive viability and competes with APS reductase to partition sulfate between the primary and secondary branches of the sulfur assimilatory pathway; however, the biochemical regulation of APSK is poorly understood. The 1.8-Å resolution crystal structure of APSR from A. thaliana (AtAPSK) in complex with β,γ-imidoadenosine-5'-triphosphate, Mg(2+), and APS provides a view of the Michaelis complex for this enzyme and reveals the presence of an intersubunit disulfide bond between Cys86 and Cys119. Functional analysis of AtAPSK demonstrates that reduction of Cys86-Cys119 resulted in a 17-fold higher k(cat)/K(m) and a 15-fold increase in K(i) for substrate inhibition by APS compared with the oxidized enzyme. The C86A/C119A mutant was kinetically similar to the reduced WT enzyme. Gel- and activity-based titrations indicate that the midpoint potential of the disulfide in AtAPSK is comparable to that observed in APS reductase. Both cysteines are invariant among the APSK from plants, but not other organisms, which suggests redox-control as a unique regulatory feature of the plant APSK. Based on structural, functional, and sequence analyses, we propose that the redox-sensitive APSK evolved after bifurcation of the sulfur assimilatory pathway in the green plant lineage and that changes in redox environment resulting from oxidative stresses may affect partitioning of APS into the primary and secondary thiol metabolic routes by having opposing effects on APSK and APS reductase in plants.
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Bhave DP, Han WG, Pazicni S, Penner-Hahn JE, Carroll KS, Noodleman L. Geometric and electrostatic study of the [4Fe-4S] cluster of adenosine-5'-phosphosulfate reductase from broken symmetry density functional calculations and extended X-ray absorption fine structure spectroscopy. Inorg Chem 2011; 50:6610-25. [PMID: 21678934 DOI: 10.1021/ic200446c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Adenosine-5'-phosphosulfate reductase (APSR) is an iron-sulfur protein that catalyzes the reduction of adenosine-5'-phosphosulfate (APS) to sulfite. APSR coordinates to a [4Fe-4S] cluster via a conserved CC-X(~80)-CXXC motif, and the cluster is essential for catalysis. Despite extensive functional, structural, and spectroscopic studies, the exact role of the iron-sulfur cluster in APS reduction remains unknown. To gain an understanding into the role of the cluster, density functional theory (DFT) analysis and extended X-ray fine structure spectroscopy (EXAFS) have been performed to reveal insights into the coordination, geometry, and electrostatics of the [4Fe-4S] cluster. X-ray absorption near-edge structure (XANES) data confirms that the cluster is in the [4Fe-4S](2+) state in both native and substrate-bound APSR while EXAFS data recorded at ~0.1 Å resolution indicates that there is no significant change in the structure of the [4Fe-4S] cluster between the native and substrate-bound forms of the protein. On the other hand, DFT calculations provide an insight into the subtle differences between the geometry of the cluster in the native and APS-bound forms of APSR. A comparison between models with and without the tandem cysteine pair coordination of the cluster suggests a role for the unique coordination in facilitating a compact geometric structure and "fine-tuning" the electronic structure to prevent reduction of the cluster. Further, calculations using models in which residue Lys144 is mutated to Ala confirm the finding that Lys144 serves as a crucial link in the interactions involving the [4Fe-4S] cluster and APS.
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Affiliation(s)
- Devayani P Bhave
- Chemical Biology Graduate Program, University of Michigan, Ann Arbor, Michigan 48109-2216, USA
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Curreem SO, Teng JL, Tse H, Yuen KY, Lau SK, Woo PC. General metabolism of Laribacter hongkongensis: a genome-wide analysis. Cell Biosci 2011; 1:16. [PMID: 21711917 PMCID: PMC3125206 DOI: 10.1186/2045-3701-1-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Accepted: 04/19/2011] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Laribacter hongkongensis is associated with community-acquired gastroenteritis and traveler's diarrhea. In this study, we performed an in-depth annotation of the genes and pathways of the general metabolism of L. hongkongensis and correlated them with its phenotypic characteristics. RESULTS The L. hongkongensis genome possesses the pentose phosphate and gluconeogenesis pathways and tricarboxylic acid and glyoxylate cycles, but incomplete Embden-Meyerhof-Parnas and Entner-Doudoroff pathways, in agreement with its asaccharolytic phenotype. It contains enzymes for biosynthesis and β-oxidation of saturated fatty acids, biosynthesis of all 20 universal amino acids and selenocysteine, the latter not observed in Neisseria gonorrhoeae, Neisseria meningitidis and Chromobacterium violaceum. The genome contains a variety of dehydrogenases, enabling it to utilize different substrates as electron donors. It encodes three terminal cytochrome oxidases for respiration using oxygen as the electron acceptor under aerobic and microaerophilic conditions and four reductases for respiration with alternative electron acceptors under anaerobic conditions. The presence of complete tetrathionate reductase operon may confer survival advantage in mammalian host in association with diarrhea. The genome contains CDSs for incorporating sulfur and nitrogen by sulfate assimilation, ammonia assimilation and nitrate reduction. The existence of both glutamate dehydrogenase and glutamine synthetase/glutamate synthase pathways suggests an importance of ammonia metabolism in the living environments that it may encounter. CONCLUSIONS The L. hongkongensis genome possesses a variety of genes and pathways for carbohydrate, amino acid and lipid metabolism, respiratory chain and sulfur and nitrogen metabolism. These allow the bacterium to utilize various substrates for energy production and survive in different environmental niches.
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Affiliation(s)
- Shirly O Curreem
- Department of Microbiology, The University of Hong Kong, Hong Kong.
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Lee JS, White E, Kim SG, Schlesinger SR, Lee SY, Kim SK. Discovery of a novel adenosine 5′-phosphosulfate (APS) reductase from the methanarcheon Methanocaldococcus jannaschii. Process Biochem 2011. [DOI: 10.1016/j.procbio.2010.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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