1
|
Hendrix J, Epperson LE, Tong EI, Chan YL, Hasan NA, Dawrs SN, Norton GJ, Virdi R, Crooks JL, Chan ED, Honda JR, Strong M. Complete genome assembly of Hawai'i environmental nontuberculous mycobacteria reveals unexpected co-isolation with methylobacteria. PLoS One 2023; 18:e0291072. [PMID: 37703253 PMCID: PMC10499228 DOI: 10.1371/journal.pone.0291072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 08/22/2023] [Indexed: 09/15/2023] Open
Abstract
Nontuberculous mycobacteria (NTM) are ubiquitous environmental opportunistic pathogens that can cause chronic lung disease. Within the United States, Hawai'i has the highest incidence of NTM lung disease, though the precise reasons are yet to be fully elucidated. One possibility is the high prevalence of NTM in the Hawai'i environment acting as a potential reservoir for opportunistic NTM infections. Through our previous initiatives to collect and characterize NTM in Hawai'i, community scientists of Hawai'i have collected thousands of environmental samples for sequencing. Here, these community scientists were invited for the first time into a high school lab in O'ahu for a genomic sequencing workshop, where participants sequenced four of the collected isolate genomic samples using the Oxford Nanopore Technologies MinION sequencer. Participants generated high quality long read data that when combined with short read Illumina data yielded complete bacterial genomic assemblies suitable for in-depth analysis. The gene annotation analysis identified a suite of genes that might help NTM thrive in the Hawai'i environment. Further, we found evidence of co-occurring methylobacteria, revealed from the sequencing data, suggesting that in some cases methylobacteria and NTM may coexist in the same niche, challenging previously accepted paradigms. The sequencing efforts presented here generated novel insights regarding the potential survival strategies and microbial interactions of NTM in the geographic hot spot of Hawai'i. We highlight the contributions of community scientists and present an activity that can be reimplemented as a workshop or classroom activity by other research groups to engage their local communities.
Collapse
Affiliation(s)
- Jo Hendrix
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States of America
- Computational Bioscience Program, University of Colorado, Anschutz Medical Campus, Aurora, CO, United States of America
| | - L. Elaine Epperson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States of America
| | - Eric I. Tong
- ‘Iolani School, Honolulu, Hawai’i, United States of America
| | - Yvonne L. Chan
- ‘Iolani School, Honolulu, Hawai’i, United States of America
| | - Nabeeh A. Hasan
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States of America
| | - Stephanie N. Dawrs
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States of America
| | - Grant J. Norton
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States of America
| | - Ravleen Virdi
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States of America
| | - James L. Crooks
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, CO, United States of America
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, United States of America
| | - Edward D. Chan
- Department of Medicine and Academic Affairs, National Jewish Health, Denver, CO, United States of America
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
- Department of Medicine, Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, CO, United States of America
| | - Jennifer R. Honda
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas Health Science Center at Tyler, Tyler, TX, United States of America
| | - Michael Strong
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States of America
- Computational Bioscience Program, University of Colorado, Anschutz Medical Campus, Aurora, CO, United States of America
| |
Collapse
|
2
|
Pis Diez CM, Antelo GT, Dalia TN, Dalia AB, Giedroc DP, Capdevila DA. Increased intracellular persulfide levels attenuate HlyU-mediated hemolysin transcriptional activation in Vibrio cholerae. J Biol Chem 2023; 299:105147. [PMID: 37567478 PMCID: PMC10509353 DOI: 10.1016/j.jbc.2023.105147] [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: 03/14/2023] [Revised: 07/20/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023] Open
Abstract
The vertebrate host's immune system and resident commensal bacteria deploy a range of highly reactive small molecules that provide a barrier against infections by microbial pathogens. Gut pathogens, such as Vibrio cholerae, sense and respond to these stressors by modulating the expression of exotoxins that are crucial for colonization. Here, we employ mass spectrometry-based profiling, metabolomics, expression assays, and biophysical approaches to show that transcriptional activation of the hemolysin gene hlyA in V. cholerae is regulated by intracellular forms of sulfur with sulfur-sulfur bonds, termed reactive sulfur species (RSS). We first present a comprehensive sequence similarity network analysis of the arsenic repressor superfamily of transcriptional regulators, where RSS and hydrogen peroxide sensors segregate into distinct clusters of sequences. We show that HlyU, transcriptional activator of hlyA in V. cholerae, belongs to the RSS-sensing cluster and readily reacts with organic persulfides, showing no reactivity or DNA dissociation following treatment with glutathione disulfide or hydrogen peroxide. Surprisingly, in V. cholerae cell cultures, both sulfide and peroxide treatment downregulate HlyU-dependent transcriptional activation of hlyA. However, RSS metabolite profiling shows that both sulfide and peroxide treatment raise the endogenous inorganic sulfide and disulfide levels to a similar extent, accounting for this crosstalk, and confirming that V. cholerae attenuates HlyU-mediated activation of hlyA in a specific response to intracellular RSS. These findings provide new evidence that gut pathogens may harness RSS-sensing as an evolutionary adaptation that allows them to overcome the gut inflammatory response by modulating the expression of exotoxins.
Collapse
Affiliation(s)
- Cristian M Pis Diez
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), Buenos Aires, Argentina; Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Giuliano T Antelo
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), Buenos Aires, Argentina; Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Triana N Dalia
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Ankur B Dalia
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA.
| | - Daiana A Capdevila
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), Buenos Aires, Argentina.
| |
Collapse
|
3
|
Pis Diez CM, Antelo GT, Dalia TN, Dalia AB, Giedroc DP, Capdevila DA. Increased intracellular persulfide levels attenuate HlyU-mediated hemolysin transcriptional activation in Vibrio cholerae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.13.532278. [PMID: 36993174 PMCID: PMC10054925 DOI: 10.1101/2023.03.13.532278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The vertebrate host’s immune system and resident commensal bacteria deploy a range of highly reactive small molecules that provide a barrier against infections by microbial pathogens. Gut pathogens, such as Vibrio cholerae , sense and respond to these stressors by modulating the expression of exotoxins that are crucial for colonization. Here, we employ mass-spectrometry-based profiling, metabolomics, expression assays and biophysical approaches to show that transcriptional activation of the hemolysin gene hlyA in V. cholerae is regulated by intracellular reactive sulfur species (RSS), specifically sulfane sulfur. We first present a comprehensive sequence similarity network analysis of the arsenic repressor (ArsR) superfamily of transcriptional regulators where RSS and reactive oxygen species (ROS) sensors segregate into distinct clusters. We show that HlyU, transcriptional activator of hlyA in V. cholerae , belongs to the RSS-sensing cluster and readily reacts with organic persulfides, showing no reactivity and remaining DNA-bound following treatment with various ROS in vitro, including H 2 O 2 . Surprisingly, in V. cholerae cell cultures, both sulfide and peroxide treatment downregulate HlyU-dependent transcriptional activation of hlyA . However, RSS metabolite profiling shows that both sulfide and peroxide treatment raise the endogenous inorganic sulfide and disulfide levels to a similar extent, accounting for this crosstalk, and confirming that V. cholerae attenuates HlyU-mediated activation of hlyA in a specific response to intracellular RSS. These findings provide new evidence that gut pathogens may harness RSS-sensing as an evolutionary adaptation that allows them to overcome the gut inflammatory response by modulating the expression of exotoxins.
Collapse
Affiliation(s)
- Cristian M. Pis Diez
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), C1405BWE Ciudad Autónoma de, Buenos Aires, Argentina
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Giuliano T. Antelo
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), C1405BWE Ciudad Autónoma de, Buenos Aires, Argentina
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Triana N. Dalia
- Department of Biology, Indiana University, Bloomington, IN 47405-7102, USA
| | - Ankur B. Dalia
- Department of Biology, Indiana University, Bloomington, IN 47405-7102, USA
| | - David P. Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Daiana A. Capdevila
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), C1405BWE Ciudad Autónoma de, Buenos Aires, Argentina
| |
Collapse
|
4
|
Yu Y, Xie Z, Yang J, Yang R, Li Y, Zhu Y, Zhao Y, Yang Q, Chen J, Alwathnani HA, Feng R, Rensing C, Herzberg M. Citrobacter portucalensis Sb-2 contains a metalloid resistance determinant transmitted by Citrobacter phage Chris1. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130184. [PMID: 36270189 DOI: 10.1016/j.jhazmat.2022.130184] [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: 09/01/2022] [Revised: 10/05/2022] [Accepted: 10/10/2022] [Indexed: 05/25/2023]
Abstract
Bacterial adaptation to extreme environments is often mediated by horizontal gene transfer (HGT) via genetic mobile elements. Nevertheless, phage-mediated HGT conferring bacterial arsenic resistance determinants has rarely been investigated. In this study, a highly arsenite and antimonite resistant bacterium, Citrobacter portucalensis strain Sb-2, was isolated, and genome analysis showed that several putative arsenite and antimonite resistance determinants were flanked or embedded in prophages. Furthermore, an active bacteriophage carrying one of the ars clusters (arsRDABC arsR-yraQ/arsP) was obtained and sequenced. These genes encoding putative arsenic resistance determinants were induced by arsenic and antimony as demonstrated by RT-qPCR, and one gene arsP/yraQ of the ars cluster was shown to give resistance to MAs(III) and Rox(III), thereby showing function. Here, we were able to directly show that these phage-mediated arsenic and antimony resistances play a significant role in adapting to As- and Sb-contaminated environments. In addition, we demonstrate that this phage is responsible for conferring arsenic and antimony resistances to C. portucalensis strain Sb-2.
Collapse
Affiliation(s)
- Yanshuang Yu
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Zhenchen Xie
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Jigang Yang
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Ruixiang Yang
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yuanping Li
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yongguan Zhu
- State Key Laboratory of Regional and Urban Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Yanlin Zhao
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Qiue Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jichen Chen
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350002, China
| | - Hend A Alwathnani
- Department of Botany and Microbiology, King Saud University, Riyadh, Saudi Arabia
| | - Renwei Feng
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.
| | - Martin Herzberg
- Molecular Microbiology, Institute for Biology/Microbiology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle(Saale), Germany
| |
Collapse
|
5
|
Ares Á, Sakai S, Sasaki T, Shimamura S, Mitarai S, Nunoura T. Sequestration and efflux largely account for cadmium and copper resistance in the deep-sea Nitratiruptor sp. SB155-2 (phylum Campylobacterota). Environ Microbiol 2022; 24:6144-6163. [PMID: 36284406 PMCID: PMC10092412 DOI: 10.1111/1462-2920.16255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/20/2022] [Indexed: 01/12/2023]
Abstract
In deep-sea hydrothermal vent environments, metal-enriched fluids and sediments abound, making these habitats ideal to study metal resistance in prokaryotes. In this investigation, we employed transcriptomics and shotgun proteomics with scanning transmission electron microscopy and energy-dispersive x-ray spectroscopy (STEM-EDX) to better understand mechanisms of tolerance for cadmium (Cd) and copper (Cu) at stress-inducing concentrations in Nitratiruptor sp. SB155-2 (phylum Campylobacterota). Transcriptomic profiles were remarkably different in the presence of these two metals, displaying 385 (19%) and 629 (31%) differentially transcribed genes (DTG) in the presence of Cd(II) and Cu(II), respectively, while only 7% of differentially transcribed (DT) genes were shared, with genes for non-specific metal transporters and genes involved in oxidative stress-response predominating. Transcriptomic and proteomic analyses confirmed that metal-specific DT pathways under Cu(II) stress, including those involving sulfur, cysteine, and methionine, are likely required for high-affinity efflux systems, while flagella formation and chemotaxis were over-represented under Cd(II) stress. Consistent with these differences, STEM-EDX analysis revealed that polyphosphate-like granules (pPLG), the formation of CdS particles, and the periplasmic space are crucial for Cd(II) sequestration. Overall, this study provides new insights regarding metal-specific adaptations of Campylobacterota to deep-sea hydrothermal vent environments.
Collapse
Affiliation(s)
- Ángela Ares
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Sanae Sakai
- Super-Cutting-Edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Japan
| | - Toshio Sasaki
- Imaging section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Shigeru Shimamura
- Super-Cutting-Edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Japan
| | - Satoshi Mitarai
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Takuro Nunoura
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| |
Collapse
|
6
|
Li J, Cui M, Zhao J, Wang J, Fang X. A self-amplifying plasmid based ultrasensitive biosensor for the detection of As(Ⅲ) in water. Biosens Bioelectron 2022; 221:114937. [DOI: 10.1016/j.bios.2022.114937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022]
|
7
|
Cloning and functional characterization of arsenite oxidase (aoxB) gene associated with arsenic transformation in Pseudomonas sp. strain AK9. Gene X 2022; 850:146926. [DOI: 10.1016/j.gene.2022.146926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 11/22/2022] Open
|
8
|
Stefanini I, Di Paola M, Liti G, Marranci A, Sebastiani F, Casalone E, Cavalieri D. Resistance to Arsenite and Arsenate in Saccharomyces cerevisiae Arises through the Subtelomeric Expansion of a Cluster of Yeast Genes. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19138119. [PMID: 35805774 PMCID: PMC9266342 DOI: 10.3390/ijerph19138119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/25/2022] [Accepted: 06/28/2022] [Indexed: 01/25/2023]
Abstract
Arsenic is one of the most prevalent toxic elements in the environment, and its toxicity affects every organism. Arsenic resistance has mainly been observed in microorganisms, and, in bacteria, it has been associated with the presence of the Ars operon. In Saccharomyces cerevisiae, three genes confer arsenic resistance: ARR1, ARR2, and ARR3. Unlike bacteria, in which the presence of the Ars genes confers per se resistance to arsenic, most of the S. cerevisiae isolates present the three ARR genes, regardless of whether the strain is resistant or sensitive to arsenic. To assess the genetic features that make natural S. cerevisiae strains resistant to arsenic, we used a combination of comparative genomic hybridization, whole-genome sequencing, and transcriptomics profiling with microarray analyses. We observed that both the presence and the genomic location of multiple copies of the whole cluster of ARR genes were central to the escape from subtelomeric silencing and the acquisition of resistance to arsenic. As a result of the repositioning, the ARR genes were expressed even in the absence of arsenic. In addition to their relevance in improving our understanding of the mechanism of arsenic resistance in yeast, these results provide evidence for a new cluster of functionally related genes that are independently duplicated and translocated.
Collapse
Affiliation(s)
- Irene Stefanini
- Department of Life Sciences and Systems Biology, University of Turin, 10123 Turin, Italy;
| | - Monica Di Paola
- Department of Biology, University of Florence, Sesto Fiorentino, 50019 Florence, Italy; (M.D.P.); (E.C.)
| | - Gianni Liti
- National Centre for Scientific Research (CNRS), National Institute of Health and Medical Research (INSERM), Institute for Research on Cancer and Aging (IRCAN), Université Côte d’Azur, 06103 Nice, France;
| | - Andrea Marranci
- Core Research Laboratory, Oncogenomics Unit, Istituto di Fisiologia Clinica, Institute for Cancer Research and Pre-vention (ISPRO), 56124 Pisa, Italy;
| | - Federico Sebastiani
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Sesto Fiorentino, 50019 Florence, Italy;
| | - Enrico Casalone
- Department of Biology, University of Florence, Sesto Fiorentino, 50019 Florence, Italy; (M.D.P.); (E.C.)
| | - Duccio Cavalieri
- Department of Biology, University of Florence, Sesto Fiorentino, 50019 Florence, Italy; (M.D.P.); (E.C.)
- Correspondence:
| |
Collapse
|
9
|
Glodowska M, Welte CU, Kurth JM. Metabolic potential of anaerobic methane oxidizing archaea for a broad spectrum of electron acceptors. Adv Microb Physiol 2022; 80:157-201. [PMID: 35489791 DOI: 10.1016/bs.ampbs.2022.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Methane (CH4) is a potent greenhouse gas significantly contributing to the climate warming we are currently facing. Microorganisms play an important role in the global CH4 cycle that is controlled by the balance between anaerobic production via methanogenesis and CH4 removal via methanotrophic oxidation. Research in recent decades advanced our understanding of CH4 oxidation, which until 1976 was believed to be a strictly aerobic process. Anaerobic oxidation of methane (AOM) coupled to sulfate reduction is now known to be an important sink of CH4 in marine ecosystems. Furthermore, in 2006 it was discovered that anaerobic CH4 oxidation can also be coupled to nitrate reduction (N-DAMO), demonstrating that AOM may be much more versatile than previously thought and linked to other electron acceptors. In consequence, an increasing number of studies in recent years showed or suggested that alternative electron acceptors can be used in the AOM process including FeIII, MnIV, AsV, CrVI, SeVI, SbV, VV, and BrV. In addition, humic substances as well as biochar and perchlorate (ClO4-) were suggested to mediate AOM. Anaerobic methanotrophic archaea, the so-called ANME archaea, are key players in the AOM process, yet we are still lacking deeper understanding of their metabolism, electron acceptor preferences and their interaction with other microbial community members. It is still not clear whether ANME archaea can oxidize CH4 and reduce metallic electron acceptors independently or via electron transfer to syntrophic partners, interspecies electron transfer, nanowires or conductive pili. Therefore, the aim of this review is to summarize and discuss the current state of knowledge about ANME archaea, focusing on their physiology, metabolic flexibility and potential to use various electron acceptors.
Collapse
Affiliation(s)
- Martyna Glodowska
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands.
| | - Cornelia U Welte
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands.
| | - Julia M Kurth
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| |
Collapse
|
10
|
Biochemical, molecular and in silico characterization of arsenate reductase from Bacillus thuringiensis KPWP1 tolerant to salt, arsenic and a wide range of pH. Arch Microbiol 2021; 204:46. [DOI: 10.1007/s00203-021-02660-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 01/03/2023]
|
11
|
Chen F, Luo Y, Li C, Wang J, Chen L, Zhong X, Zhang B, Zhu Q, Zou R, Guo X, Zhou Y, Guo L. Sub-chronic low-dose arsenic in rice exposure induces gut microbiome perturbations in mice. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 227:112934. [PMID: 34755630 DOI: 10.1016/j.ecoenv.2021.112934] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 10/14/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
Long-term consumption of arsenic-contaminated rice has become a public health issue that urgently needs to be addressed. In this study, mice were exposed to arsenic in rice (low dose, 0.91 mg/kg; medium dose, 9.1 mg/kg) for 30 days and 60 days, respectively, and the effects on pathological structures of spleen and skin, as well as the structure of the fecal microbiome were examined. The findings revealed dose/time cumulative effects on pathological changes, with even a low dose exposure for 30 days causing destruction of splenic follicular structure and thickening of dermal keratinized and epidermal layers. The Firmicutes/Bacteroidetes ratio in the community and the positive/negative ratio in network links were higher in arsenic groups, suggesting that arsenic resulted in a less healthy and unstable microbiome for the host. Thus lifetime consumption of arsenic in rice may have potential health effects on humans and must be carefully assessed to safeguard human health. Furthermore, in arsenic groups, arsenic-resistant bacteria or arsenic hazards remediation bacteria changed to be the dominant bacteria and acted as the core bacteria in the network modules. Some microbial arsenic transforming genes (arsC, arsR, arsA, ACR3, and aoxB) differed, indicating that the gut microbiome changed to withstand arsenic stress. Furthermore, Faecalibaculum, Lachnospiraceae_NK4A136_group, Angelakisella, Ruminiclostridium, and Desulfovibrionaceae are positively associated with arsenic dosage and may be useful in the early detection of arsenicals.
Collapse
Affiliation(s)
- Fubin Chen
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Guangdong 523808, China.
| | - Yu Luo
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Guangdong 523808, China.
| | - Chengji Li
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Guangdong 523808, China.
| | - Jiating Wang
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Guangdong 523808, China; Guangdong Provincial Key Laboratory of Food, Nutrition and Health; Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China..
| | - Linkang Chen
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Guangdong 523808, China.
| | - Xiaoting Zhong
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Guangdong 523808, China.
| | - Bin Zhang
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Guangdong 523808, China.
| | - Qijiong Zhu
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Guangdong 523808, China.
| | - Rong Zou
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Guangdong 523808, China.
| | - Xuming Guo
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Guangdong 523808, China.
| | - Yubin Zhou
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Guangdong 523808, China; Guangdong Provincial Key Laboratory of Research and Development of Natural Drugs, and School of Pharmacy, Guangdong Medical University, Dongguan 523808, PR China.
| | - Lianxian Guo
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Guangdong 523808, China.
| |
Collapse
|
12
|
Overview on the role of heavy metals tolerance on developing antibiotic resistance in both Gram-negative and Gram-positive bacteria. Arch Microbiol 2021; 203:2761-2770. [PMID: 33811263 DOI: 10.1007/s00203-021-02275-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 02/11/2021] [Accepted: 03/10/2021] [Indexed: 12/26/2022]
Abstract
Environmental health is a critical concern, continuously contaminated by physical and biological components (viz., anthropogenic activity), which adversely affect on biodiversity, ecosystems and human health. Nonetheless, environmental pollution has great impact on microbial communities, especially bacteria, which try to evolve in changing environment. For instance, during the course of adaptation, bacteria easily become resistance to antibiotics and heavy metals. Antibiotic resistance genes are now one of the most vital pollutants, provided as a source of frequent horizontal gene transfer. In this review, the environmental cause of multidrug resistance (MDR) that was supposed to be driven by either heavy metals or combination of environmental factors was essentially reviewed, especially focussed on the correlation between accumulation of heavy metals and development of MDR by bacteria. This kind of correlation was seemed to be non-significant, i.e. paradoxical. Gram-positive bacteria accumulating much of toxic heavy metal (i.e. highly stress tolerance) were unlikely to become MDR, whereas Gram-negative bacteria that often avoid accumulation of toxic heavy metal by efflux pump systems were come out to be more prone to MDR. So far, other than antibiotic contaminant, no such available data strongly support the direct influence of heavy metals in bacterial evolution of MDR; combinations of factors may drive the evolution of antibiotic resistance. Therefore, Gram-positive bacteria are most likely to be an efficient member in treatment of industrial waste water, especially in the removal of heavy metals, perhaps inducing the less chance of antibiotic resistance pollution in the environment.
Collapse
|
13
|
Dash B, Sahu N, Singh AK, Gupta SB, Soni R. Arsenic efflux in Enterobacter cloacae RSN3 isolated from arsenic-rich soil. Folia Microbiol (Praha) 2020; 66:189-196. [PMID: 33131029 DOI: 10.1007/s12223-020-00832-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/30/2020] [Indexed: 11/28/2022]
Abstract
In the present study, bacterial isolates were screened for arsenic resistance efficiency. Environmental isolates were isolated from arsenic-rich soil samples (i.e., from Rajnandgaon district of Chhattisgarh state, India). Amplification and sequencing of 16S rRNA gene revealed that the isolates were of Bacillus firmus RSN1, Brevibacterium senegalense RSN2, Enterobacter cloacae RSN3, Stenotrophomonas pavanii RSN6, Achromobacter mucicolens RSN7, and Ochrobactrum intermedium RSN10. Arsenite efflux gene (arsB) was successfully amplified in E. cloacae RSN3. Atomic absorption spectroscopy (AAS) analysis showed an absorption of 32.22% arsenic by the RSN3 strain. Furthermore, results of scanning electron microscopy (SEM) for morphological variations revealed an initial increase in the cell size at 1 mM sodium arsenate; however, it was decreased at 10 mM concentration in comparison to control. This change of the cell size in different metal concentrations was due to the uptake and expulsion of the metal from the cell, which also confirmed the arsenite efflux system.
Collapse
Affiliation(s)
- Biplab Dash
- Department of Agricultural Microbiology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Krishak Nagar Jora, Raipur, 492012, CG, India
| | - Narayan Sahu
- Department of Agricultural Microbiology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Krishak Nagar Jora, Raipur, 492012, CG, India
| | - Anup Kumar Singh
- Department of Agricultural Microbiology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Krishak Nagar Jora, Raipur, 492012, CG, India
| | - S B Gupta
- Department of Agricultural Microbiology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Krishak Nagar Jora, Raipur, 492012, CG, India
| | - Ravindra Soni
- Department of Agricultural Microbiology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Krishak Nagar Jora, Raipur, 492012, CG, India.
| |
Collapse
|
14
|
Mazumder P, Sharma SK, Taki K, Kalamdhad AS, Kumar M. Microbes involved in arsenic mobilization and respiration: a review on isolation, identification, isolates and implications. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2020; 42:3443-3469. [PMID: 32170513 DOI: 10.1007/s10653-020-00549-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 02/29/2020] [Indexed: 06/10/2023]
Abstract
Microorganisms play an important role in arsenic (As) cycling in the environment. Microbes mobilize As directly or indirectly, and natural/geochemical processes such as sulphate and iron reduction, oxidative sulphide mineral dissolution, arsenite (AsO33-) oxidation and arsenate (AsO43-) respiration further aid in As cycle in the environment. Arsenate serves as an electron donor for the microbes during anaerobic conditions in the sediment. The present work reviews the recent development in As contamination, various As-metabolizing microbes and their phylogenetic diversity, to understand the role of microbial communities in As respiration and mobilization. It also summarizes the contemporary understanding of the intricate biochemistry and molecular biology of natural As metabolisms. Some successful examples of engineered microbes by harnessing these natural mechanisms for effective remediation are also discussed. The study indicates that there is an exigent need to have a clear understanding of environmental aspects of As mobilization and subsequent oxidation-reduction by a suitable microbial consortium.
Collapse
Affiliation(s)
- Payal Mazumder
- Centre for the Environment, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Subhash Kumar Sharma
- Environmental Engineering, National Institute of Technology, Tiruchirappalli, Tamil Nadu, India
| | - Kaling Taki
- Discipline of Civil Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, 382355, India
| | - Ajay S Kalamdhad
- Department of Civil Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Manish Kumar
- Discipline of Earth Sciences, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, 382355, India.
| |
Collapse
|
15
|
|
16
|
Ryan MP, Slattery S, Pembroke JT. A Novel Arsenate-Resistant Determinant Associated with ICEpMERPH, a Member of the SXT/R391 Group of Mobile Genetic Elements. Genes (Basel) 2019; 10:genes10121048. [PMID: 31888308 PMCID: PMC6947025 DOI: 10.3390/genes10121048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 12/17/2022] Open
Abstract
ICEpMERPH, the first integrative conjugative element (ICE) of the SXT/R391 family isolated in the United Kingdom and Europe, was analyzed to determine the nature of its adaptive functions, its genetic structure, and its homology to related elements normally found in pathogenic Vibrio or Proteus species. Whole genome sequencing of Escherichia coli (E. coli) isolate K802 (which contains the ICEpMERPH) was carried out using Illumina sequencing technology. ICEpMERPH has a size of 110 Kb and 112 putative open reading frames (ORFs). The “hotspot regions” of the element were found to contain putative restriction digestion systems, insertion sequences, and heavy metal resistance genes that encoded resistance to mercury, as previously reported, but also surprisingly to arsenate. A novel arsenate resistance system was identified in hotspot 4 of the element, unrelated to other SXT/R391 elements. This arsenate resistance system was potentially linked to two genes: orf69, encoding an organoarsenical efflux major facilitator superfamily (MFS) transporter-like protein related to ArsJ, and orf70, encoding nicotinamide adenine dinucleotide (NAD)-dependent glyceraldehyde-3-phosphate dehydrogenase. Phenotypic analysis using isogenic strains of Escherichia coli strain AB1157 with and without the ICEpMERPH revealed resistance to low levels of arsenate in the range of 1–5 mM. This novel, low-level resistance may have an important adaptive function in polluted environments, which often contain low levels of arsenate contamination. A bioinformatic analysis on the novel determinant and the phylogeny of ICEpMERPH was presented.
Collapse
|
17
|
Shi LD, Chen YS, Du JJ, Hu YQ, Shapleigh JP, Zhao HP. Metagenomic Evidence for a Methylocystis Species Capable of Bioremediation of Diverse Heavy Metals. Front Microbiol 2019; 9:3297. [PMID: 30687279 PMCID: PMC6333641 DOI: 10.3389/fmicb.2018.03297] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 12/18/2018] [Indexed: 02/01/2023] Open
Abstract
Heavy metal pollution has become an increasingly serious problem worldwide. Co-contamination with toxic mercury (Hg) and arsenic (As) presents a particularly difficult bioremediation trouble. By oxidizing the greenhouse gas methane, methanotrophs have been demonstrated to have high denitrification activity in eutrophic waters, indicating their possible potential for use in bioremediation of Hg(II) and As(V) in polluted water. Using metagenomics, a novel Methylocystis species (HL18), which was one of the most prevalent bacteria (9.9% of the relative abundance) in a CH4-based bio-reactor, is described here. The metagenomic-assembled genome (MAG) HL18 had gene products whose average amino acid identity against other known Methylocystis species varied from 69 to 85%, higher than the genus threshold but lower than the species boundary. Genomic analysis indicated that HL18 possessed all the genes necessary for the reduction of Hg(II) and As(V). Phylogenetic investigation of mercuric reductase (MerA) found that the HL18 protein was most closely affiliated with proteins from two Hg(II)-reducing bacteria, Bradyrhizobium sp. strain CCH5-F6 and Paracoccus halophilus. The genomic organization and phylogeny of the genes in the As(V)-reducing operon (arsRCCB) had significant identity with those from a As(V)-reducing bacterium belonging to the Rhodopseudomonas genus, indicating their reduction capability of As(V). Further analysis found that at least eight genera of methanotrophs possess both Hg(II) and As(V) reductases, illustrating the generally overlooked metabolic potential of methanotrophs. These results suggest that methanotrophs have greater bioremediation potential in heavy metal contaminated water than has been appreciated and could play an important role in the mitigation of heavy metal toxicity of contaminated wastewater.
Collapse
Affiliation(s)
- Ling-Dong Shi
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.,Zhejiang Province Key Laboratory for Water Pollution Control and Environment, Zhejiang University, Hangzhou, China.,MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Yu-Shi Chen
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Jia-Jie Du
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Yi-Qing Hu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - James P Shapleigh
- Department of Microbiology, Cornell University, Ithaca, NY, United States
| | - He-Ping Zhao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.,Zhejiang Province Key Laboratory for Water Pollution Control and Environment, Zhejiang University, Hangzhou, China.,MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| |
Collapse
|
18
|
Chauhan D, Srivastava PA, Agnihotri V, Yennamalli RM, Priyadarshini R. Structure and function prediction of arsenate reductase from Deinococcus indicus DR1. J Mol Model 2019; 25:15. [PMID: 30610463 DOI: 10.1007/s00894-018-3885-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/28/2018] [Indexed: 12/01/2022]
Abstract
Arsenic prevalence in the environment impelled many organisms to develop resistance over the course of evolution. Tolerance to arsenic, either as the pentavalent [As(V)] form or the trivalent form [As(III)], by bacteria has been well studied in prokaryotes, and the mechanism of action is well defined. However, in the rod-shaped arsenic tolerant Deinococcus indicus DR1, the key enzyme, arsenate reductase (ArsC) has not been well studied. ArsC of D. indicus belongs to the Grx-linked prokaryotic arsenate reductase family. While it shares homology with the well-studied ArsC of Escherichia coli having a catalytic cysteine (Cys 12) and arginine triad (Arg 60, 94, and 107), the active site of D.indicus ArsC contains four residues Glu 9, Asp 53, Arg 86, and Glu 100, and with complete absence of structurally equivalent residue for crucial Cys 12. Here, we report that the mechanism of action of ArsC of D. indicus is different as a result of convergent evolution and most likely able to detoxify As(V) using a mix of positively- and negatively-charged residues in its active site, unlike the residues of E. coli. This suggests toward the possibility of an alternative mechanism of As (V) degradation in bacteria.
Collapse
Affiliation(s)
- Deepika Chauhan
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh, India
| | - Pulkit A Srivastava
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Himachal Pradesh, 173234, India
| | - Vidushi Agnihotri
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Himachal Pradesh, 173234, India
| | - Ragothaman M Yennamalli
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Himachal Pradesh, 173234, India.
| | - Richa Priyadarshini
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh, India.
| |
Collapse
|
19
|
Sekizuka T, Matsui M, Takahashi T, Hayashi M, Suzuki S, Tokaji A, Kuroda M. Complete Genome Sequence of bla IMP-6-Positive Metakosakonia sp. MRY16-398 Isolate From the Ascites of a Diverticulitis Patient. Front Microbiol 2018; 9:2853. [PMID: 30524415 PMCID: PMC6262049 DOI: 10.3389/fmicb.2018.02853] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/06/2018] [Indexed: 01/09/2023] Open
Abstract
A novel species of carbapenemase-producing Enterobacteriaceae (CPE) was isolated from a patient diagnosed with sigmoid colon diverticulitis. At first, laboratory testing suggested it was Klebsiella oxytoca or Pantoea sp.; however, a complete genome sequence of the isolate, MRY16-398, revealed that it could be novel species, most similar to [Kluyvera] intestini, of which taxonomic nomenclature is still under discussion. Orthologous conserved gene analysis among 42 related bacterial strains indicated that MRY16-398 was classified as the newly proposed genus Metakosakonia. Further, MRY16-398 was found to harbor the blaIMP-6 gene-positive class 1 integron (In722) in plasmid pMRY16-398_2 (IncN replicon, 47.4 kb in size). This finding implies that rare and opportunistic bacteria could be potential infectious agents. In conclusion, our results highlight the need for continuous monitoring for CPE even in nonpathogenic bacteria in the nosocomial environment.
Collapse
Affiliation(s)
- Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mari Matsui
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Japan
| | - Tomiyo Takahashi
- The Public Health Institute of Kochi Prefecture, Kōchi City, Japan
| | - Michiko Hayashi
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Japan
| | - Satowa Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Japan
| | - Akihiko Tokaji
- The Public Health Institute of Kochi Prefecture, Kōchi City, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| |
Collapse
|
20
|
Chellamuthu P, Tran F, Silva KPT, Chavez MS, El-Naggar MY, Boedicker JQ. Engineering bacteria for biogenic synthesis of chalcogenide nanomaterials. Microb Biotechnol 2018; 12:161-172. [PMID: 30369058 PMCID: PMC6302716 DOI: 10.1111/1751-7915.13320] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 09/10/2018] [Indexed: 11/30/2022] Open
Abstract
Microbes naturally build nanoscale structures, including structures assembled from inorganic materials. Here, we combine the natural capabilities of microbes with engineered genetic control circuits to demonstrate the ability to control biological synthesis of chalcogenide nanomaterials in a heterologous host. We transferred reductase genes from both Shewanella sp. ANA-3 and Salmonella enterica serovar Typhimurium into a heterologous host (Escherichia coli) and examined the mechanisms that regulate the properties of biogenic nanomaterials. Expression of arsenate reductase genes and thiosulfate reductase genes in E. coli resulted in the synthesis of arsenic sulfide nanomaterials. In addition to processing the starting materials via redox enzymes, cellular components also nucleated the formation of arsenic sulfide nanomaterials. The shape of the nanomaterial was influenced by the bacterial culture, with the synthetic E. coli strain producing nanospheres and conditioned media or cultures of wild-type Shewanella sp. producing nanofibres. The diameter of these nanofibres also depended on the biological context of synthesis. These results demonstrate the potential for biogenic synthesis of nanomaterials with controlled properties by combining the natural capabilities of wild microbes with the tools from synthetic biology.
Collapse
Affiliation(s)
- Prithiviraj Chellamuthu
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA, USA.,Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Frances Tran
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA, USA.,Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Kalinga Pavan T Silva
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA, USA
| | - Marko S Chavez
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA, USA
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA, USA.,Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.,Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - James Q Boedicker
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA, USA.,Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
21
|
Sekizuka T, Yatsu K, Inamine Y, Segawa T, Nishio M, Kishi N, Kuroda M. Complete Genome Sequence of a blaKPC-2-Positive Klebsiella pneumoniae Strain Isolated from the Effluent of an Urban Sewage Treatment Plant in Japan. mSphere 2018; 3:e00314-18. [PMID: 30232165 PMCID: PMC6147131 DOI: 10.1128/msphere.00314-18] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 08/16/2018] [Indexed: 02/06/2023] Open
Abstract
Antimicrobial resistance genes (ARGs) and the bacteria that harbor them are widely distributed in the environment, especially in surface water, sewage treatment plant effluent, soil, and animal waste. In this study, we isolated a KPC-2-producing Klebsiella pneumoniae strain (GSU10-3) from a sampling site in Tokyo Bay, Japan, near a wastewater treatment plant (WWTP) and determined its complete genome sequence. Strain GSU10-3 is resistant to most β-lactam antibiotics and other antimicrobial agents (quinolones and aminoglycosides). This strain is classified as sequence type 11 (ST11), and a core genome phylogenetic analysis indicated that strain GSU10-3 is closely related to KPC-2-positive Chinese clinical isolates from 2011 to 2017 and is clearly distinct from strains isolated from the European Union (EU), United States, and other Asian countries. Strain GSU10-3 harbors four plasmids, including a blaKPC-2-positive plasmid, pGSU10-3-3 (66.2 kb), which is smaller than other blaKPC-2-positive plasmids and notably carries dual replicons (IncFII [pHN7A8] and IncN). Such downsizing and the presence of dual replicons may promote its maintenance and stable replication, contributing to its broad host range with low fitness costs. A second plasmid, pGSU10-3-1 (159.0 kb), an IncA/C2 replicon, carries a class 1 integron (containing intI1, dfrA12, aadA2, qacEΔ1, and sul1) with a high degree of similarity to a broad-host-range plasmid present in the family Enterobacteriaceae The plasmid pGSU10-3-2 (134.8 kb), an IncFII(K) replicon, carries the IS26-mediated ARGs [aac(6')Ib-cr,blaOXA-1, catB4 (truncated), and aac(3)-IId], tet(A), and a copper/arsenate resistance locus. GSU10-3 is the first nonclinical KPC-2-producing environmental Enterobacteriaceae isolate from Japan for which the whole genome has been sequenced.IMPORTANCE We isolated and determined the complete genome sequence of a KPC-2-producing K. pneumoniae strain from a sampling site in Tokyo Bay, Japan, near a wastewater treatment plant (WWTP). In Japan, the KPC type has been very rarely detected, while IMP is the most predominant type of carbapenemase in clinical carbapenemase-producing Enterobacteriaceae (CPE) isolates. Although laboratory testing thus far suggested that Japan may be virtually free of KPC-producing Enterobacteriaceae, we have detected it from effluent from a WWTP. Antimicrobial resistance (AMR) monitoring of WWTP effluent may contribute to the early detection of future AMR bacterial dissemination in clinical settings and communities; indeed, it will help illuminate the whole picture in which environmental contamination through WWTP effluent plays a part.
Collapse
Affiliation(s)
- Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Toyama, Tokyo, Japan
| | - Koji Yatsu
- Pathogen Genomics Center, National Institute of Infectious Diseases, Toyama, Tokyo, Japan
| | - Yuba Inamine
- Pathogen Genomics Center, National Institute of Infectious Diseases, Toyama, Tokyo, Japan
| | - Takaya Segawa
- Pathogen Genomics Center, National Institute of Infectious Diseases, Toyama, Tokyo, Japan
| | - Miho Nishio
- Pathogen Genomics Center, National Institute of Infectious Diseases, Toyama, Tokyo, Japan
| | - Norimi Kishi
- Pathogen Genomics Center, National Institute of Infectious Diseases, Toyama, Tokyo, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Toyama, Tokyo, Japan
| |
Collapse
|
22
|
Aye SL, Fujiwara K, Doi N. A dual system using compartmentalized partnered replication for selection of arsenic-responsive transcriptional regulator. J Biochem 2018; 164:341-348. [DOI: 10.1093/jb/mvy055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/06/2018] [Indexed: 01/29/2023] Open
Affiliation(s)
- Seaim Lwin Aye
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, Japan
| | - Kei Fujiwara
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, Japan
| | - Nobuhide Doi
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, Japan
| |
Collapse
|
23
|
Nazemi E, Hassen WM, Frost EH, Dubowski JJ. Growth of Escherichia coli on the GaAs (001) surface. Talanta 2018; 178:69-77. [PMID: 29136882 DOI: 10.1016/j.talanta.2017.08.097] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/23/2017] [Accepted: 08/24/2017] [Indexed: 10/18/2022]
Abstract
Detection of pathogenic bacteria and monitoring their susceptibility to antibiotics are of great importance in the fields of medicine, pharmaceutical research, as well as water and food industries. In order to develop a photonic biosensor for detection of bacteria by taking advantage of photoluminescence (PL) of GaAs-based devices, we have investigated the capture and growth of Escherichia coli K12 on bare and biofunctionalized surfaces of GaAs (001) - a material of interest for capping different semiconductor microstructures. The results were compared with the capture and growth of Escherichia coli K12 on Au surfaces that have commonly been applied for studying a variety of biological and biochemical reactions. We found that neither GaAs nor Au-coated glass wafers placed in Petri dishes inoculated with bacteria inhibited bacterial growth in nutrient agar, regardless of the wafers being bare or biofunctionalized. However, the capture and growth of bacteria on biofunctionalized surfaces of GaAs and Au wafers kept in a flow cell and exposed to different concentrations of bacteria and growth medium revealed that the initial surface coverage and the subsequent bacterial growth were dependent on the biofunctionalization architecture, with antibody-coated surfaces clearly being most efficient in capturing bacteria and offering better conditions for growth of bacteria. We have observed that, as long as the GaAs wafers were exposed to bacterial suspensions at concentrations of at least 105 CFU/mL, bacteria could grow on the surface of wafers, regardless of the type of biofunctionalization architecture used to capture the bacteria. These results provide important insight towards the successful development of GaAs-based devices designed for photonic monitoring of bacterial reactions to different biochemical environments.
Collapse
Affiliation(s)
- Elnaz Nazemi
- Interdisciplinary Institute for Technological Innovation (3IT), CNRS UMI-3463, Department of Electrical and Computer Engineering, Faculty of Engineering, Université de Sherbrooke, 3000, boul. de l'Université, Sherbrooke, Québec, Canada J1K 0A5.
| | - Walid M Hassen
- Interdisciplinary Institute for Technological Innovation (3IT), CNRS UMI-3463, Department of Electrical and Computer Engineering, Faculty of Engineering, Université de Sherbrooke, 3000, boul. de l'Université, Sherbrooke, Québec, Canada J1K 0A5.
| | - Eric H Frost
- Interdisciplinary Institute for Technological Innovation (3IT), CNRS UMI-3463, Department of Electrical and Computer Engineering, Faculty of Engineering, Université de Sherbrooke, 3000, boul. de l'Université, Sherbrooke, Québec, Canada J1K 0A5; Department of Microbiology and Infectiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001, 12th Avenue North, Sherbrooke, Québec, Canada J1H 5N4.
| | - Jan J Dubowski
- Interdisciplinary Institute for Technological Innovation (3IT), CNRS UMI-3463, Department of Electrical and Computer Engineering, Faculty of Engineering, Université de Sherbrooke, 3000, boul. de l'Université, Sherbrooke, Québec, Canada J1K 0A5.
| |
Collapse
|
24
|
Abbas G, Murtaza B, Bibi I, Shahid M, Niazi NK, Khan MI, Amjad M, Hussain M, Natasha. Arsenic Uptake, Toxicity, Detoxification, and Speciation in Plants: Physiological, Biochemical, and Molecular Aspects. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:E59. [PMID: 29301332 PMCID: PMC5800158 DOI: 10.3390/ijerph15010059] [Citation(s) in RCA: 322] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 12/28/2017] [Accepted: 12/30/2017] [Indexed: 11/16/2022]
Abstract
Environmental contamination with arsenic (As) is a global environmental, agricultural and health issue due to the highly toxic and carcinogenic nature of As. Exposure of plants to As, even at very low concentration, can cause many morphological, physiological, and biochemical changes. The recent research on As in the soil-plant system indicates that As toxicity to plants varies with its speciation in plants (e.g., arsenite, As(III); arsenate, As(V)), with the type of plant species, and with other soil factors controlling As accumulation in plants. Various plant species have different mechanisms of As(III) or As(V) uptake, toxicity, and detoxification. This review briefly describes the sources and global extent of As contamination and As speciation in soil. We discuss different mechanisms responsible for As(III) and As(V) uptake, toxicity, and detoxification in plants, at physiological, biochemical, and molecular levels. This review highlights the importance of the As-induced generation of reactive oxygen species (ROS), as well as their damaging impacts on plants at biochemical, genetic, and molecular levels. The role of different enzymatic (superoxide dismutase, catalase, glutathione reductase, and ascorbate peroxidase) and non-enzymatic (salicylic acid, proline, phytochelatins, glutathione, nitric oxide, and phosphorous) substances under As(III/V) stress have been delineated via conceptual models showing As translocation and toxicity pathways in plant species. Significantly, this review addresses the current, albeit partially understood, emerging aspects on (i) As-induced physiological, biochemical, and genotoxic mechanisms and responses in plants and (ii) the roles of different molecules in modulation of As-induced toxicities in plants. We also provide insight on some important research gaps that need to be filled to advance our scientific understanding in this area of research on As in soil-plant systems.
Collapse
Affiliation(s)
- Ghulam Abbas
- Department of Environmental Sciences, COMSATS Institute of Information Technology, Vehari-61100, Pakistan; (G.A.); (B.M.); (M.A.); (N.)
| | - Behzad Murtaza
- Department of Environmental Sciences, COMSATS Institute of Information Technology, Vehari-61100, Pakistan; (G.A.); (B.M.); (M.A.); (N.)
| | - Irshad Bibi
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan; (I.B.); (M.I.K.); (M.H.)
- MARUM and Department of Geosciences, University of Bremen, D-28359 Bremen, Germany
| | - Muhammad Shahid
- Department of Environmental Sciences, COMSATS Institute of Information Technology, Vehari-61100, Pakistan; (G.A.); (B.M.); (M.A.); (N.)
| | - Nabeel Khan Niazi
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan; (I.B.); (M.I.K.); (M.H.)
- MARUM and Department of Geosciences, University of Bremen, D-28359 Bremen, Germany
- Southern Cross GeoScience, Southern Cross University, Lismore 2480, Australia
| | - Muhammad Imran Khan
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan; (I.B.); (M.I.K.); (M.H.)
| | - Muhammad Amjad
- Department of Environmental Sciences, COMSATS Institute of Information Technology, Vehari-61100, Pakistan; (G.A.); (B.M.); (M.A.); (N.)
| | - Munawar Hussain
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan; (I.B.); (M.I.K.); (M.H.)
| | - Natasha
- Department of Environmental Sciences, COMSATS Institute of Information Technology, Vehari-61100, Pakistan; (G.A.); (B.M.); (M.A.); (N.)
| |
Collapse
|
25
|
Pierart A, Dumat C, Maes AQ, Sejalon-Delmas N. Influence of arbuscular mycorrhizal fungi on antimony phyto-uptake and compartmentation in vegetables cultivated in urban gardens. CHEMOSPHERE 2018; 191:272-279. [PMID: 29040941 DOI: 10.1016/j.chemosphere.2017.10.058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 09/18/2017] [Accepted: 10/09/2017] [Indexed: 05/16/2023]
Abstract
UNLABELLED 1. CONTEXT Urban areas are often contaminated with various forms of persistent metal (loid) and emerging contaminants such as antimony (Sb). Thus, in the context of urban agriculture where sustainable practices such as biofertilizers application (arbuscular mycorrhizal fungi, AMF) could improve nutrient transfer from the soil to the vegetables, the effect of AMF on metal (loid) mobility and human bioaccessibility is still poorly known. 2. METHODS The role of AMF in Sb uptake by lettuce and carrot grown in artificial substrate spiked with different Sb chemical species was investigated. Plants were grown under hydroponic conditions and half of the treatments received a concentrated spore solution to obtain mycorrhized and non-mycorrhized plants. Three weeks before harvest, plants were exposed to 10 mg.L-1 of either Sb2O3 or KSbO-tartrate (KSb). 3. RESULTS The presence of AMF significantly increased its accumulation in carrots (all organs) with higher accumulation in roots. In lettuce, accumulation appeared to be dependent on the Sb chemical species. Moreover, it was observed for the first time that AMF changed the human bioaccessible fraction of Sb in edible organs. 4. IMPLICATIONS The present results highlight a possible risk of Sb transfer from soil to edible plants cultivated in soil naturally containing AMF propagules, or when AMF are added as biofertilizers. After validating the influence of soil environment and AMF on Sb behavior in the field, these results should be considered in health risk assessments.
Collapse
Affiliation(s)
- Antoine Pierart
- Ecolab, Université de Toulouse, CNRS, INPT, UPS, Avenue de l'Agrobiopole, 31326 Auzeville-Tolosane, France.
| | - Camille Dumat
- CERTOP, CNRS, UT2J, UPS, 5 Allée Antonio Machado, 31000 Toulouse, France; Université de Toulouse, INPT, 5 Allée Antonio Machado, 31000 Toulouse, France
| | - Arthur QuyManh Maes
- LRSV, Université de Toulouse, UPS, CNRS, 24 Chemin de Borde Rouge, 31326 Castanet-Tolosan, France
| | - Nathalie Sejalon-Delmas
- LRSV, Université de Toulouse, UPS, CNRS, 24 Chemin de Borde Rouge, 31326 Castanet-Tolosan, France
| |
Collapse
|
26
|
Draft Genome Sequence of the Arsenic-Resistant Bacterium Brevundimonas denitrificans TAR-002 T. GENOME ANNOUNCEMENTS 2017; 5:5/47/e01326-17. [PMID: 29167254 PMCID: PMC5701479 DOI: 10.1128/genomea.01326-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We report the 3.2-Mb draft genome sequence of Brevundimonas denitrificans strain TAR-002T, isolated from deep-sea floor sediment. The draft genome sequence of strain TAR-002T consists of 3,231,216 bp in 44 contigs, with a G+C content of 68.47%, 3,866 potential coding sequences (CDSs), 3 rRNAs, and 45 tRNAs.
Collapse
|
27
|
Liu Y, Zhang Z, Li Y, Wen Y, Fei Y. Response of soil microbial communities to roxarsone pollution along a concentration gradient. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2017; 52:819-827. [PMID: 28276888 DOI: 10.1080/10934529.2017.1281687] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The extensive use of roxarsone (3-nitro-4-hydroxyphenylarsonic acid) as a feed additive in the broiler poultry industry can lead to environmental arsenic contamination. This study was conducted to reveal the response of soil microbial communities to roxarsone pollution along a concentration gradient. To explore the degradation process and degradation kinetics of roxarsone concentration gradients in soil, the concentration shift of roxarsone at initial concentrations of 0, 50, 100, and 200 mg/kg, as well as that of the arsenic derivatives, was detected. The soil microbial community composition and structure accompanying roxarsone degradation were investigated by high-throughput sequencing. The results showed that roxarsone degradation was inhibited by a biological inhibitor, confirming that soil microbes were absolutely essential to its degradation. Moreover, soil microbes had considerable potential to degrade roxarsone, as a high initial concentration of roxarsone resulted in a substantially increased degradation rate. The concentrations of the degradation products HAPA (3-amino-4-hydroxyphenylarsonic acid), AS(III), and AS(V) in soils were significantly positively correlated. The soil microbial community composition and structure changed significantly across the roxarsone contamination gradient, and the addition of roxarsone decreased the microbial diversity. Some bacteria tended to be inhibited by roxarsone, while Bacillus, Paenibacillus, Arthrobacter, Lysobacter, and Alkaliphilus played important roles in roxarsone degradation. Moreover, HAPA, AS(III), and AS(V) were significantly positively correlated with Symbiobacterium, which dominated soils containing roxarsone, and their abundance increased with increasing initial roxarsone concentration. Accordingly, Symbiobacterium could serve as indicator of arsenic derivatives released by roxarsone as well as the initial roxarsone concentration. This is the first investigation of microbes closely related to roxarsone degradation.
Collapse
Affiliation(s)
- Yaci Liu
- a Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences , Shijiazhuang , China
- b Key Laboratory of Groundwater Remediation of Hebei Province and China Geological Survey , Shijiazhuang, Hebei , China
| | - Zhaoji Zhang
- a Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences , Shijiazhuang , China
| | - Yasong Li
- a Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences , Shijiazhuang , China
- c CSIRO Land and Water , Urrbrae , South Australia , Australia
| | - Yi Wen
- d Department of Water Environmental Planning , Chinese Academy for Environmental Planning , Beijing , China
| | - Yuhong Fei
- a Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences , Shijiazhuang , China
| |
Collapse
|
28
|
Rovetto F, Carlier A, Van den Abeele AM, Illeghems K, Van Nieuwerburgh F, Cocolin L, Houf K. Characterization of the emerging zoonotic pathogen Arcobacter thereius by whole genome sequencing and comparative genomics. PLoS One 2017; 12:e0180493. [PMID: 28671965 PMCID: PMC5495459 DOI: 10.1371/journal.pone.0180493] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 06/17/2017] [Indexed: 11/24/2022] Open
Abstract
Four Arcobacter species have been associated with human disease, and based on current knowledge, these Gram negative bacteria are considered as potential food and waterborne zoonotic pathogens. At present, only the genome of the species Arcobacter butzleri has been analysed, and still little is known about their physiology and genetics. The species Arcobacter thereius has first been isolated from tissue of aborted piglets, duck and pig faeces, and recently from stool of human patients with enteritis. In the present study, the complete genome and analysis of the A. thereius type strain LMG24486T, as well as the comparative genome analysis with 8 other A. thereius strains are presented. Genome analysis revealed metabolic pathways for the utilization of amino acids, which represent the main source of energy, together with the presence of genes encoding for respiration-associated and chemotaxis proteins. Comparative genome analysis with the A. butzleri type strain RM4018 revealed a large correlation, though also unique features. Furthermore, in silico DDH and ANI based analysis of the nine A. thereius strains disclosed clustering into two closely related genotypes. No discriminatory differences in genome content nor phenotypic behaviour were detected, though recently the species Arcobacter porcinus was proposed to encompass part of the formerly identified Arcobacter thereius strains. The report of the presence of virulence associated genes in A. thereius, the presence of antibiotic resistance genes, verified by in vitro susceptibility testing, as well as other pathogenic related relevant features, support the classification of A. thereius as an emerging pathogen.
Collapse
Affiliation(s)
- Francesca Rovetto
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, Merelbeke, Belgium
- Department of Forestry, Agriculture and Food Sciences, University of Torino, Largo Braccini 2, Grugliasco, Italy
| | - Aurélien Carlier
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, Ghent, Belgium
| | | | - Koen Illeghems
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, Merelbeke, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, Ghent, Belgium
| | - Luca Cocolin
- Department of Forestry, Agriculture and Food Sciences, University of Torino, Largo Braccini 2, Grugliasco, Italy
| | - Kurt Houf
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, Merelbeke, Belgium
| |
Collapse
|
29
|
Berset Y, Merulla D, Joublin A, Hatzimanikatis V, van der Meer JR. Mechanistic Modeling of Genetic Circuits for ArsR Arsenic Regulation. ACS Synth Biol 2017; 6:862-874. [PMID: 28215088 DOI: 10.1021/acssynbio.6b00364] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Bioreporters are living cells that generate an easily measurable signal in the presence of a chemical compound. They acquire their functionality from synthetic gene circuits, the configuration of which defines the response signal and signal-to-noise ratio. Bioreporters based on the Escherichia coli ArsR system have raised significant interest for quantifying arsenic pollution, but they need to be carefully optimized to accurately work in the required low concentration range (1-10 μg arsenite L-1). To better understand the general functioning of ArsR-based genetic circuits, we developed a comprehensive mechanistic model that was empirically tested and validated in E. coli carrying different circuit configurations. The model accounts for the different elements in the circuits (proteins, DNA, chemical species), and their detailed affinities and interactions, and predicts the (fluorescent) output from the bioreporter cell as a function of arsenite concentration. The model was parametrized using existing ArsR biochemical data, and then complemented by parameter estimations from the accompanying experimental data using a scatter search algorithm. Model predictions and experimental data were largely coherent for feedback and uncoupled circuit configurations, different ArsR alleles, promoter strengths, and presence or absence of arsenic efflux in the bioreporters. Interestingly, the model predicted a particular useful circuit variant having steeper response at low arsenite concentrations, which was experimentally confirmed and may be useful as arsenic bioreporter in the field. From the extensive validation we expect the mechanistic model to further be a useful framework for detailed modeling of other synthetic circuits.
Collapse
Affiliation(s)
- Yves Berset
- Department
of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
- Laboratory
of Computational Systems Biotechnology, Ecole Polytechnique Fédérale de Lausane (EPFL), CH 1015 Lausanne, Switzerland
| | - Davide Merulla
- Department
of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Aurélie Joublin
- Department
of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Vassily Hatzimanikatis
- Laboratory
of Computational Systems Biotechnology, Ecole Polytechnique Fédérale de Lausane (EPFL), CH 1015 Lausanne, Switzerland
| | - Jan R. van der Meer
- Department
of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| |
Collapse
|
30
|
Saha RP, Samanta S, Patra S, Sarkar D, Saha A, Singh MK. Metal homeostasis in bacteria: the role of ArsR-SmtB family of transcriptional repressors in combating varying metal concentrations in the environment. Biometals 2017; 30:459-503. [PMID: 28512703 DOI: 10.1007/s10534-017-0020-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 05/09/2017] [Indexed: 02/02/2023]
Abstract
Bacterial infections cause severe medical problems worldwide, resulting in considerable death and loss of capital. With the ever-increasing rise of antibiotic-resistant bacteria and the lack of development of new antibiotics, research on metal-based antimicrobial therapy has now gained pace. Metal ions are essential for survival, but can be highly toxic to organisms if their concentrations are not strictly controlled. Through evolution, bacteria have acquired complex metal-management systems that allow them to acquire metals that they need for survival in different challenging environments while evading metal toxicity. Metalloproteins that controls these elaborate systems in the cell, and linked to key virulence factors, are promising targets for the anti-bacterial drug development. Among several metal-sensory transcriptional regulators, the ArsR-SmtB family displays greatest diversity with several distinct metal-binding and nonmetal-binding motifs that have been characterized. These prokaryotic metolloregulatory transcriptional repressors represses the expression of operons linked to stress-inducing concentrations of metal ions by directly binding to the regulatory regions of DNA, while derepression results from direct binding of metal ions by these homodimeric proteins. Many bacteria, e.g., Mycobacterium tuberculosis, Bacillus anthracis, etc., have evolved to acquire multiple metal-sensory motifs which clearly demonstrate the importance of regulating concentrations of multiple metal ions. Here, we discussed the mechanisms of how ArsR-SmtB family regulates the intracellular bioavailability of metal ions both inside and outside of the host. Knowledge of the metal-challenges faced by bacterial pathogens and their survival strategies will enable us to develop the next generation drugs.
Collapse
Affiliation(s)
- Rudra P Saha
- Department of Biotechnology, School of Biotechnology, Adamas University, Kolkata, 700126, India.
| | - Saikat Samanta
- Department of Microbiology, School of Science, Adamas University, Kolkata, 700126, India
| | - Surajit Patra
- Department of Biotechnology, School of Biotechnology, Adamas University, Kolkata, 700126, India
| | - Diganta Sarkar
- Department of Biotechnology, Techno India University, Kolkata, 700091, India
| | - Abinit Saha
- Department of Biotechnology, School of Biotechnology, Adamas University, Kolkata, 700126, India
| | - Manoj Kumar Singh
- Department of Biotechnology, School of Biotechnology, Adamas University, Kolkata, 700126, India
| |
Collapse
|
31
|
Liu Y, Zhang Z, Li Y, Fei Y. Response of microbial communities to roxarsone under different culture conditions. Can J Microbiol 2017; 63:661-670. [PMID: 28177786 DOI: 10.1139/cjm-2016-0652] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Roxarsone is a feed additive widely used in the broiler and swine industries that has the potential to contaminate the environment, mainly via the use of poultry manure as fertilizer, which results in release of inorganic arsenic to the soil and water. This study was conducted to investigate roxarsone degradation and the response of the microbial community under different culture conditions using high-throughput sequencing technology. Poultry litter was incubated for 288 h in the presence of roxarsone under light aerobic, dark aerobic, or dark anaerobic conditions. The results showed that roxarsone was completely degraded after 48 h of dark anaerobic incubation, while 79.9% and 94.5% of roxarsone was degraded after 288 h of dark aerobic and light aerobic incubation, respectively. Under dark aerobic conditions with microbial inhibitor sodium azide, roxarsone was rarely degraded during the 288 h of incubation, illustrating that microorganisms play an important role in roxarsone degradation. Microbial community structure was significantly different among various culture conditions. Olivibacter, Sphingobacterium, and Proteiniphilum were the top 3 genera in the control samples. Sphingobacterium and Alishewanella dominated the light aerobic samples, while the dominant microflora of the dark aerobic samples were Acinetobacter spp. Pseudomonas and Advenella were the predominant genera of dark anaerobic samples. This study emphasizes the potential importance of microbes in roxarsone degradation and expands our current understanding of microbial ecology during roxarsone degradation under different environmental conditions.
Collapse
Affiliation(s)
- Yaci Liu
- a Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang, Hebei 050061, People's Republic of China.,b Key Laboratory of Groundwater Remediation of Hebei Province and China Geological Survey, Shijiazhuang, Hebei 050061, People's Republic of China
| | - Zhaoji Zhang
- a Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang, Hebei 050061, People's Republic of China
| | - Yasong Li
- a Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang, Hebei 050061, People's Republic of China.,b Key Laboratory of Groundwater Remediation of Hebei Province and China Geological Survey, Shijiazhuang, Hebei 050061, People's Republic of China.,c CSIRO Land and Water, Urrbrae, South Australia 5064, Australia
| | - Yuhong Fei
- a Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang, Hebei 050061, People's Republic of China
| |
Collapse
|
32
|
Verma PK, Verma S, Meher AK, Pande V, Mallick S, Bansiwal AK, Tripathi RD, Dhankher OP, Chakrabarty D. Overexpression of rice glutaredoxins (OsGrxs) significantly reduces arsenite accumulation by maintaining glutathione pool and modulating aquaporins in yeast. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 106:208-17. [PMID: 27174139 DOI: 10.1016/j.plaphy.2016.04.052] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 04/29/2016] [Accepted: 04/29/2016] [Indexed: 05/05/2023]
Abstract
Arsenic (As) is an acute poison and class I carcinogen, can cause a serious health risk. Staple crops like rice are the primary source of As contamination in human food. Rice grown on As contaminated areas accumulates higher As in their edible parts. Based on our previous transcriptome data, two rice glutaredoxins (OsGrx_C7 and OsGrx_C2.1) were identified that showed up-regulated expression during As stress. Here, we report OsGrx_C7 and OsGrx_C2.1 from rice involved in the regulation of intracellular arsenite (AsIII). To elucidate the mechanism of OsGrx mediated As tolerance, both OsGrxs were cloned and expressed in Escherichia coli (Δars) and Saccharomyces cerevisiae mutant strains (Δycf1, Δacr3). The expression of OsGrxs increased As tolerance in E. coli (Δars) mutant strain (up to 4 mM AsV and up to 0.6 mM AsIII). During AsIII exposure, S. cerevisiae (Δacr3) harboring OsGrx_C7 and OsGrx_C2.1 have lower intracellular AsIII accumulation (up to 30.43% and 24.90%, respectively), compared to vector control. Arsenic accumulation in As-sensitive S. cerevisiae mutant (Δycf1) also reduced significantly on exposure to inorganic As. The expression of OsGrxs in yeast maintained intracellular GSH pool and increased extracellular GSH concentration. Purified OsGrxs displays in vitro GSH-disulfide oxidoreductase, glutathione reductase and arsenate reductase activities. Also, both OsGrxs are involved in AsIII extrusion by altering the Fps1 transcripts in yeast and protect the cell by maintaining cellular GSH pool. Thus, our results strongly suggest that OsGrxs play a crucial role in the maintenance of the intracellular GSH pool and redox status of the cell during both AsV and AsIII stress and might be involved in regulating intracellular AsIII levels by modulation of aquaporin expression and functions.
Collapse
Affiliation(s)
- Pankaj Kumar Verma
- Genetics and Molecular Biology Division, CSIR-National Botanical Research Institute, India; Department of Biotechnology, Kumaun University, India
| | - Shikha Verma
- Genetics and Molecular Biology Division, CSIR-National Botanical Research Institute, India; Department of Biotechnology, Kumaun University, India
| | - Alok Kumar Meher
- Environmental Material Division, CSIR-National Environmental Engineering Research Institute, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, India
| | - Shekhar Mallick
- Environmental Biotechnology Division, CSIR-National Botanical Research Institute, India
| | - Amit Kumar Bansiwal
- Environmental Material Division, CSIR-National Environmental Engineering Research Institute, India
| | - Rudra Deo Tripathi
- Environmental Biotechnology Division, CSIR-National Botanical Research Institute, India
| | - Om Parkash Dhankher
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA, USA
| | - Debasis Chakrabarty
- Genetics and Molecular Biology Division, CSIR-National Botanical Research Institute, India.
| |
Collapse
|
33
|
Characterization of the Neisseria gonorrhoeae Iron and Fur Regulatory Network. J Bacteriol 2016; 198:2180-91. [PMID: 27246574 DOI: 10.1128/jb.00166-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 05/24/2016] [Indexed: 01/05/2023] Open
Abstract
UNLABELLED The Neisseria gonorrhoeae ferric uptake regulator (Fur) protein controls expression of iron homeostasis genes in response to intracellular iron levels. In this study, using transcriptome sequencing (RNA-seq) analysis of an N. gonorrhoeae fur strain, we defined the gonococcal Fur and iron regulons and characterized Fur-controlled expression of an ArsR-like DNA binding protein. We observed that 158 genes (8% of the genome) showed differential expression in response to iron in an N. gonorrhoeae wild-type or fur strain, while 54 genes exhibited differential expression in response to Fur. The Fur regulon was extended to additional regulators, including NrrF and 13 other small RNAs (sRNAs), and two transcriptional factors. One transcriptional factor, coding for an ArsR-like regulator (ArsR), exhibited increased expression under iron-replete conditions in the wild-type strain but showed decreased expression across iron conditions in the fur strain, an effect that was reversed in a fur-complemented strain. Fur was shown to bind to the promoter region of the arsR gene downstream of a predicted σ(70) promoter region. Electrophoretic mobility shift assay (EMSA) analysis confirmed binding of the ArsR protein to the norB promoter region, and sequence analysis identified two additional putative targets, NGO1411 and NGO1646. A gonococcal arsR strain demonstrated decreased survival in human endocervical epithelial cells compared to that of the wild-type and arsR-complemented strains, suggesting that the ArsR regulon includes genes required for survival in host cells. Collectively, these results demonstrate that the N. gonorrhoeae Fur functions as a global regulatory protein to repress or activate expression of a large repertoire of genes, including additional transcriptional regulatory proteins. IMPORTANCE Gene regulation in bacteria in response to environmental stimuli, including iron, is of paramount importance to both bacterial replication and, in the case of pathogenic bacteria, successful infection. Bacterial DNA binding proteins are a common mechanism utilized by pathogens to control gene expression under various environmental conditions. Here, we show that the DNA binding protein Fur, expressed by the human pathogen Neisseria gonorrhoeae, controls the expression of a large repertoire of genes and extends this regulon by controlling expression of additional DNA binding proteins. One of these proteins, an ArsR-like regulator, was required for N. gonorrhoeae survival within host cells. These results show that the Fur regulon extends to additional regulatory proteins, which together contribute to gonococcal mechanisms of pathogenesis.
Collapse
|
34
|
Jiang D, Liu Y, Wang A, Zhang G, Yang G, Chen Y, Ji P, Liu C, Song Y, Su Y, Wang G, Wang J, Zhao B, Deng R. High level soluble expression and one-step purification of IBDV VP2 protein in Escherichia coli. Biotechnol Lett 2016; 38:901-8. [PMID: 27003577 DOI: 10.1007/s10529-016-2073-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 03/01/2016] [Indexed: 11/24/2022]
Abstract
OBJECTIVES To improve the expression of soluble IBDV VP2 protein by using different tagged vectors in Escherichia coli. RESULTS Fusion tags, Grifin, MBP, SUMO, thioredoxin, γ-crystallin, ArsC and PpiB, enhanced the expression and solubility of VP2 protein. The fusion proteins were purified by Ni-NTA chromatography, MBP-VP2 showed the highest purity about 90 %. After removing the MBP tag, VP2 self-assembled into virus-like particles, ~25 nm diam. Results from AGP suggested the recombinant IBDV VP2 protein identified by reference serum like IBDV. CONCLUSION All the seven tags enhanced the expression and solubility of IBDV VP2 protein. The recombinant protein self-assembly into virus like particles and possess antigenicity as reference IBDV.
Collapse
Affiliation(s)
- Dawei Jiang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, People's Republic of China.,Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China
| | - Yunchao Liu
- Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China
| | - Aiping Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, People's Republic of China
| | - Gaiping Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, People's Republic of China. .,Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China.
| | - Guoyu Yang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, People's Republic of China
| | - Yumei Chen
- Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China.,School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, People's Republic of China
| | - Pengchao Ji
- Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China
| | - Chang Liu
- Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China
| | - Yapeng Song
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, People's Republic of China.,Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China
| | - Yunfang Su
- Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China
| | - Guoqiang Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, People's Republic of China.,Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China
| | - Jucai Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, People's Republic of China.,Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China
| | - Baolei Zhao
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, People's Republic of China.,Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China
| | - Ruiguang Deng
- Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China
| |
Collapse
|
35
|
Yoon Y, Kim S, Chae Y, Jeong SW, An YJ. Evaluation of bioavailable arsenic and remediation performance using a whole-cell bioreporter. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 547:125-131. [PMID: 26780137 DOI: 10.1016/j.scitotenv.2015.12.141] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 12/28/2015] [Accepted: 12/29/2015] [Indexed: 06/05/2023]
Abstract
The traditional method of evaluating the effects of soil contaminants on living organisms by measuring the total amount of contaminant has been largely inadequate, in part because testing contamination levels is hindered in real samples. Here we report a novel strategy for testing arsenic (As) bioavailability in soil samples by direct (in vivo) and indirect (in vitro) measurement using an Escherichia coli-based whole-cell bioreporter (WCB). The WCB was used to test As-amended Landwirtschaftliche Untersuchungs und Forschungsanstalt soils as well as field soils collected from a smelter area under remediation in order to evaluate the efficiency of bioavailable As removal. The percentage of bioavailable As in amended and field soils was 5.8% (range: 4.9%-7.6%) and 0.6% (0.08%-1.09%) of total As, respectively. In contaminated soils, total As was decreased, whereas bioavailable As was slightly increased after soil washing. These results emphasize the importance of considering ecotoxicological aspects of soil remediation; to this end, the WCB is a useful tool for evaluating the efficiency of soil remediation by assessing bioavailability along with the total amount of contaminant present.
Collapse
Affiliation(s)
- Youngdae Yoon
- Department of Environmental Health Science, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Sunghoon Kim
- Department of Environmental Health Science, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Yooeun Chae
- Department of Environmental Health Science, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Seung-Woo Jeong
- Department of Environmental Engineering, Kunsan National University, Kunsan 54150, Korea
| | - Youn-Joo An
- Department of Environmental Health Science, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea.
| |
Collapse
|
36
|
Comparative genome analysis of Lysinibacillus B1-CDA, a bacterium that accumulates arsenics. Genomics 2015; 106:384-92. [DOI: 10.1016/j.ygeno.2015.09.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 07/29/2015] [Accepted: 09/15/2015] [Indexed: 11/18/2022]
|
37
|
Abstract
This chapter focuses on transition metals. All transition metal cations are toxic-those that are essential for Escherichia coli and belong to the first transition period of the periodic system of the element and also the "toxic-only" metals with higher atomic numbers. Common themes are visible in the metabolism of these ions. First, there is transport. High-rate but low-affinity uptake systems provide a variety of cations and anions to the cells. Control of the respective systems seems to be mainly through regulation of transport activity (flux control), with control of gene expression playing only a minor role. If these systems do not provide sufficient amounts of a needed ion to the cell, genes for ATP-hydrolyzing high-affinity but low-rate uptake systems are induced, e.g., ABC transport systems or P-type ATPases. On the other hand, if the amount of an ion is in surplus, genes for efflux systems are induced. By combining different kinds of uptake and efflux systems with regulation at the levels of gene expression and transport activity, the concentration of a single ion in the cytoplasm and the composition of the cellular ion "bouquet" can be rapidly adjusted and carefully controlled. The toxicity threshold of an ion is defined by its ability to produce radicals (copper, iron, chromate), to bind to sulfide and thiol groups (copper, zinc, all cations of the second and third transition period), or to interfere with the metabolism of other ions. Iron poses an exceptional metabolic problem due its metabolic importance and the low solubility of Fe(III) compounds, combined with the ability to cause dangerous Fenton reactions. This dilemma for the cells led to the evolution of sophisticated multi-channel iron uptake and storage pathways to prevent the occurrence of unbound iron in the cytoplasm. Toxic metals like Cd2+ bind to thiols and sulfide, preventing assembly of iron complexes and releasing the metal from iron-sulfur clusters. In the unique case of mercury, the cation can be reduced to the volatile metallic form. Interference of nickel and cobalt with iron is prevented by the low abundance of these metals in the cytoplasm and their sequestration by metal chaperones, in the case of nickel, or by B12 and its derivatives, in the case of cobalt. The most dangerous metal, copper, catalyzes Fenton-like reactions, binds to thiol groups, and interferes with iron metabolism. E. coli solves this problem probably by preventing copper uptake, combined with rapid efflux if the metal happens to enter the cytoplasm.
Collapse
|
38
|
Matsuda M, Kuribayashi T, Yamamoto S, Millar BC, Moore JE. Transformation and characterization of an arsenic gene operon from urease-positive thermophilic Campylobacter (UPTC) in Escherichia coli. Folia Microbiol (Praha) 2015; 61:57-62. [DOI: 10.1007/s12223-015-0405-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Accepted: 06/01/2015] [Indexed: 10/23/2022]
|
39
|
Wang B, Barahona M, Buck M. Amplification of small molecule-inducible gene expression via tuning of intracellular receptor densities. Nucleic Acids Res 2015; 43:1955-64. [PMID: 25589545 PMCID: PMC4330358 DOI: 10.1093/nar/gku1388] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Ligand-responsive transcription factors in prokaryotes found simple small molecule-inducible gene expression systems. These have been extensively used for regulated protein production and associated biosynthesis of fine chemicals. However, the promoter and protein engineering approaches traditionally used often pose significant restrictions to predictably and rapidly tune the expression profiles of inducible expression systems. Here, we present a new unified and rational tuning method to amplify the sensitivity and dynamic ranges of versatile small molecule-inducible expression systems. We employ a systematic variation of the concentration of intracellular receptors for transcriptional control. We show that a low density of the repressor receptor (e.g. TetR and ArsR) in the cell can significantly increase the sensitivity and dynamic range, whereas a high activator receptor (e.g. LuxR) density achieves the same outcome. The intracellular concentration of receptors can be tuned in both discrete and continuous modes by adjusting the strength of their cognate driving promoters. We exemplified this approach in several synthetic receptor-mediated sensing circuits, including a tunable cell-based arsenic sensor. The approach offers a new paradigm to predictably tune and amplify ligand-responsive gene expression with potential applications in synthetic biology and industrial biotechnology.
Collapse
Affiliation(s)
- Baojun Wang
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JR, UK
- To whom correspondence should be addressed. Tel: +44 131 650 5527; Fax: +44 131 650 8650;
| | - Mauricio Barahona
- Department of Mathematics, Faculty of Natural Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Martin Buck
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, SW7 2AZ, UK
| |
Collapse
|
40
|
Mafla S, Moraga R, León CG, Guzmán-Fierro VG, Yañez J, Smith CT, Mondaca MA, Campos VL. Biodegradation of roxarsone by a bacterial community of underground water and its toxic impact. World J Microbiol Biotechnol 2015; 31:1267-77. [PMID: 26063647 DOI: 10.1007/s11274-015-1886-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 06/05/2015] [Indexed: 02/06/2023]
Abstract
Roxarsone is included in chicken food as anticoccidial and mainly excreted unchanged in faeces. Microorganisms biotransform roxarsone into toxic compounds that leach and contaminate underground waters used for human consumption. This study evaluated roxarsone biotransformation by underground water microorganisms and the toxicity of the resulting compounds. Underground water from an agricultural field was used to prepare microcosms, containing 0.05 mM roxarsone, and cultured under aerobic or anaerobic conditions. Bacterial communities of microcosms were characterized by PCR-DGGE. Roxarsone degradation was measured by HPLC/HG/AAS. Toxicity was evaluated using HUVEC cells and the Toxi-ChromoTest kit. Roxarsone degradation analysis, after 15 days, showed that microcosms of underground water with nutrients degraded 90 and 83.3% of roxarsone under anaerobic and aerobic conditions, respectively. Microcosms without nutrients degraded 50 and 33.1% under anaerobic and aerobic conditions, respectively. Microcosms including nutrients showed more roxarsone conversion into toxic inorganic arsenic species. DGGE analyses showed the presence of Proteobacteria, Firmicutes, Actinobacteria, Planctomycetes and Spirochaetes. Toxicity assays showed that roxarsone biotransformation by underground water microorganisms in all microcosms generated degradation products toxic for eukaryotic and prokaryotic cells. Furthermore, toxicity increased when roxarsone leached though a soil column and was further transformed by the bacterial community present in underground water. Therefore, using underground water from areas where roxarsone containing manure is used as fertilizer might be a health risk.
Collapse
Affiliation(s)
- S Mafla
- Environmental Microbiology Laboratory, Department of Microbiology, Faculty of Biological Sciences, University of Concepción, P.O. Box 160-C, Correo 3, Concepción, Chile
| | | | | | | | | | | | | | | |
Collapse
|
41
|
Webster DP, TerAvest MA, Doud DF, Chakravorty A, Holmes EC, Radens CM, Sureka S, Gralnick JA, Angenent LT. An arsenic-specific biosensor with genetically engineered Shewanella oneidensis in a bioelectrochemical system. Biosens Bioelectron 2014; 62:320-4. [DOI: 10.1016/j.bios.2014.07.003] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Revised: 06/28/2014] [Accepted: 07/02/2014] [Indexed: 02/02/2023]
|
42
|
Patel HK, Matiuzzo M, Bertani I, Bigirimana VDP, Ash GJ, Höfte M, Venturi V. Identification of virulence associated loci in the emerging broad host range plant pathogen Pseudomonas fuscovaginae. BMC Microbiol 2014; 14:274. [PMID: 25394860 PMCID: PMC4237756 DOI: 10.1186/s12866-014-0274-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 10/23/2014] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Pseudomonas fuscovaginae (Pfv) is an emerging plant pathogen of rice and also of other gramineae plants. It causes sheath brown rot disease in rice with symptoms that are characterized by brown lesions on the flag leaf sheath, grain discoloration and sterility. It was first isolated as a high altitude pathogen in Japan and has since been reported in several countries throughout the world. Pfv is a broad host range pathogen and very little is known about its virulence mechanisms. RESULTS An in planta screen of 1000 random independent Tn5 genomic mutants resulted in the isolation of nine mutants which showed altered virulence. Some of these isolates are mutated for functions which are known to be virulence associated factors in other phytopathogenic bacteria (eg. pil gene, phytotoxins and T6SS) and others might represent novel virulence loci. CONCLUSIONS Being an emerging pathogen worldwide, the broad host range pathogen Pfv has not yet been studied for its virulence functions. The roles of the nine loci identified in the in planta screen are discussed in relation to pathogenicity of Pfv. In summary, this article reports a first study on the virulence of this pathogen involving in planta screening studies and suggests the presence of several virulence features with known and novel functions in the Pseudomonas group of bacteria.
Collapse
Affiliation(s)
| | - Maura Matiuzzo
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy.
| | - Iris Bertani
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy.
| | | | - Gavin J Ash
- Graham Centre for Agricultural Innovation, School of Agricultural and Wine Sciences, Charles Sturt University, Wagga Wagga, NSW, 2650, Australia.
| | - Monica Höfte
- Department of Crop Protection, Laboratory of Phytopathology, Ghent University, Coupure, Links 653, 9000, Ghent, Belgium.
| | - Vittorio Venturi
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy.
| |
Collapse
|
43
|
Isokpehi RD, Udensi UK, Simmons SS, Hollman AL, Cain AE, Olofinsae SA, Hassan OA, Kashim ZA, Enejoh OA, Fasesan DE, Nashiru O. Evaluative profiling of arsenic sensing and regulatory systems in the human microbiome project genomes. Microbiol Insights 2014; 7:25-34. [PMID: 25452698 PMCID: PMC4230230 DOI: 10.4137/mbi.s18076] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 08/18/2014] [Accepted: 08/26/2014] [Indexed: 12/21/2022] Open
Abstract
The influence of environmental chemicals including arsenic, a type 1 carcinogen, on the composition and function of the human-associated microbiota is of significance in human health and disease. We have developed a suite of bioinformatics and visual analytics methods to evaluate the availability (presence or absence) and abundance of functional annotations in a microbial genome for seven Pfam protein families: As(III)-responsive transcriptional repressor (ArsR), anion-transporting ATPase (ArsA), arsenical pump membrane protein (ArsB), arsenate reductase (ArsC), arsenical resistance operon transacting repressor (ArsD), water/glycerol transport protein (aquaporins), and universal stress protein (USP). These genes encode function for sensing and/or regulating arsenic content in the bacterial cell. The evaluative profiling strategy was applied to 3,274 genomes from which 62 genomes from 18 genera were identified to contain genes for the seven protein families. Our list included 12 genomes in the Human Microbiome Project (HMP) from the following genera: Citrobacter, Escherichia, Lactobacillus, Providencia, Rhodococcus, and Staphylococcus. Gene neighborhood analysis of the arsenic resistance operon in the genome of Bacteroides thetaiotaomicron VPI-5482, a human gut symbiont, revealed the adjacent arrangement of genes for arsenite binding/transfer (ArsD) and cytochrome c biosynthesis (DsbD_2). Visual analytics facilitated evaluation of protein annotations in 367 genomes in the phylum Bacteroidetes identified multiple genomes in which genes for ArsD and DsbD_2 were adjacently arranged. Cytochrome c, produced by a posttranslational process, consists of heme-containing proteins important for cellular energy production and signaling. Further research is desired to elucidate arsenic resistance and arsenic-mediated cellular energy production in the Bacteroidetes.
Collapse
Affiliation(s)
- Raphael D Isokpehi
- Department of Biology, Bethune-Cookman University, Daytona Beach, FL, USA
| | - Udensi K Udensi
- RCMI Center for Environmental Health, College of Science, Engineering and Technology, Jackson State University, Jackson, MS, USA
| | - Shaneka S Simmons
- Department of Biology, Jackson State University, Jackson, MS, USA. ; Department of Computer Science, Jackson State University, Jackson, MS, USA
| | | | - Antia E Cain
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Samson A Olofinsae
- H3Africa Bioinformatics Network Node, National Biotechnology Development Agency (NABDA), Abuja, Nigeria
| | - Oluwabukola A Hassan
- H3Africa Bioinformatics Network Node, National Biotechnology Development Agency (NABDA), Abuja, Nigeria
| | - Zainab A Kashim
- H3Africa Bioinformatics Network Node, National Biotechnology Development Agency (NABDA), Abuja, Nigeria
| | - Ojochenemi A Enejoh
- H3Africa Bioinformatics Network Node, National Biotechnology Development Agency (NABDA), Abuja, Nigeria
| | - Deborah E Fasesan
- H3Africa Bioinformatics Network Node, National Biotechnology Development Agency (NABDA), Abuja, Nigeria
| | - Oyekanmi Nashiru
- H3Africa Bioinformatics Network Node, National Biotechnology Development Agency (NABDA), Abuja, Nigeria
| |
Collapse
|
44
|
Kaur H, Kumar R, Babu JN, Mittal S. Advances in arsenic biosensor development--a comprehensive review. Biosens Bioelectron 2014; 63:533-545. [PMID: 25150780 DOI: 10.1016/j.bios.2014.08.003] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/21/2014] [Accepted: 08/04/2014] [Indexed: 01/23/2023]
Abstract
Biosensors are analytical devices having high sensitivity, portability, small sample requirement and ease of use for qualitative and quantitative monitoring of various analytes of human importance. Arsenic (As), owing to its widespread presence in nature and high toxicity to living creatures, requires frequent determination in water, soil, agricultural and food samples. The present review is an effort to highlight the various advancements made so far in the development of arsenic biosensors based either on recombinant whole cells or on certain arsenic-binding oligonucleotides or proteins. The role of futuristic approaches like surface plasmon resonance (SPR) and aptamer technology has also been discussed. The biomethods employed and their general mechanisms, advantages and limitations in relevance to arsenic biosensors developed so far are intended to be discussed in this review.
Collapse
Affiliation(s)
- Hardeep Kaur
- Centre for Environmental Science and Technology, Central University of Punjab, Bathinda, Punjab 151001, India.
| | - Rabindra Kumar
- Centre for Environmental Science and Technology, Central University of Punjab, Bathinda, Punjab 151001, India.
| | - J Nagendra Babu
- Centre for Environmental Science and Technology, Central University of Punjab, Bathinda, Punjab 151001, India.
| | - Sunil Mittal
- Centre for Environmental Science and Technology, Central University of Punjab, Bathinda, Punjab 151001, India.
| |
Collapse
|
45
|
Krishnani KK, Chen W, Mulchandani A. Bactericidal activity of elastin-like polypeptide biopolymer with polyhistidine domain and silver. Colloids Surf B Biointerfaces 2014; 119:66-70. [DOI: 10.1016/j.colsurfb.2014.03.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2013] [Revised: 03/10/2014] [Accepted: 03/10/2014] [Indexed: 11/25/2022]
|
46
|
Kang YS, Shi Z, Bothner B, Wang G, McDermott TR. Involvement of the Acr3 and DctA anti-porters in arsenite oxidation in Agrobacterium tumefaciens 5A. Environ Microbiol 2014; 17:1950-62. [PMID: 24674103 DOI: 10.1111/1462-2920.12468] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 03/22/2014] [Indexed: 12/01/2022]
Abstract
Microbial arsenite (AsIII) oxidation forms a critical piece of the arsenic cycle in nature, though our understanding of how and why microorganisms oxidize AsIII remains rudimentary. Our model organism Agrobacterium tumefaciens 5A contains two distinct ars operons (ars1 and ars2) that are similar in their coding region content. The ars1 operon is located nearby the aio operon that is essential for AsIII oxidation. The AsIII/H(+) anti-porters encoded by acr3-1 and acr3-2 are required for maximal AsIII and antimonite (SbIII) resistance, but acr3-1 (negatively regulated by ArsR-1) appears more active in this regard and also required for AsIII oxidation and expression of aioBA. A malate-phosphate anti-porter DctA is regulated by RpoN and AsIII, and is required for normal growth with malate as a sole carbon source. Qualitatively, a ΔdctA mutant was normal for AsIII oxidation and AsIII/SbIII resistance at metalloid concentrations inhibitory to the Δacr3-1 mutant; however, aioBA induction kinetics was significantly phase-shift delayed. Acr3 involvement in AsIII/SbIII resistance is reasonably well understood, but the role of Acr3 and DctA anti-porters in AsIII oxidation and its regulation is unexpected, and suggests that controlled AsIII trafficking across the cytoplasmic membrane is important to a process understood to occur in the periplasm.
Collapse
Affiliation(s)
- Yoon-Suk Kang
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, 59717, USA
| | - Zunji Shi
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, 59717, USA.,State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Timothy R McDermott
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, 59717, USA
| |
Collapse
|
47
|
Krumova K, Nikolovska M, Groudeva V. Characterization of Arsenic-Transforming Bacteria from Arsenic Contaminated Sites in Bulgaria. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.1080/13102818.2008.10817542] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
|
48
|
Identification of a novel membrane transporter mediating resistance to organic arsenic in Campylobacter jejuni. Antimicrob Agents Chemother 2014; 58:2021-9. [PMID: 24419344 DOI: 10.1128/aac.02137-13] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although bacterial mechanisms involved in the resistance to inorganic arsenic are well understood, the molecular basis for organic arsenic resistance has not been described. Campylobacter jejuni, a major food-borne pathogen causing gastroenteritis in humans, is highly prevalent in poultry and is reportedly resistant to the arsenic compound roxarsone (4-hydroxy-3-nitrobenzenearsonic acid), which has been used as a feed additive in the poultry industry for growth promotion. In this study, we report the identification of a novel membrane transporter (named ArsP) that contributes to organic arsenic resistance in Campylobacter. ArsP is predicted to be a membrane permease containing eight transmembrane helices, distinct from other known arsenic transporters. Analysis of multiple C. jejuni isolates from various animal species revealed that the presence of an intact arsP gene is associated with elevated resistance to roxarsone. In addition, inactivation of arsP in C. jejuni resulted in 4- and 8-fold reductions in the MICs of roxarsone and nitarsone, respectively, compared to that for the wild-type strain. Furthermore, cloning of arsP into a C. jejuni strain lacking a functional arsP gene led to 16- and 64-fold increases in the MICs of roxarsone and nitarsone, respectively. Neither mutation nor overexpression of arsP affected the MICs of inorganic arsenic, including arsenite and arsenate, in Campylobacter. Moreover, acquisition of arsP in NCTC 11168 led to accumulation of less roxarsone than the wild-type strain lacking arsP. Together, these results indicate that ArsP functions as an efflux transporter specific for extrusion of organic arsenic and contributes to the resistance to these compounds in C. jejuni.
Collapse
|
49
|
Mathews S, Reinhold D. Biosolid-borne tetracyclines and sulfonamides in plants. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:4327-4338. [PMID: 23591931 DOI: 10.1007/s11356-013-1693-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 03/28/2013] [Indexed: 06/02/2023]
Abstract
Tetracyclines and sulfonamides used in human and animal medicine are released to terrestrial ecosystems from wastewater treatment plants or by direct manure application. The interactions between plants and these antibiotics are numerous and complex, including uptake and accumulation, phytometabolism, toxicity responses, and degradation in the rhizosphere. Uptake and accumulation of antibiotics have been studied in plants such as wheat, maize, potato, vegetables, and ornamentals. Once accumulated in plant tissue, organic contaminants can be metabolized through a sequential process of transformation, conjugation through glycosylation and glutathione pathways, and ultimately sequestration into plant tissue. While studies have yet to fully elucidate the phytometabolism of tetracyclines and sulfonamides, an in-depth review of plant and mammalian studies suggest multiple potential transformation and conjugation pathways for tetracyclines and sulfonamides. The presence of contaminants in the vicinity or within the plants can elicit stress responses and defense mechanisms that can help tolerate the negative effects of contaminants. Antibiotics can change microbial communities and enzyme activity in the rhizosphere, potentially inducing microbial antibiotic resistance. On the other hand, the interaction of microbes and root exudates on pharmaceuticals in the rhizosphere can result in degradation of the parent molecule to less toxic compounds. To fully characterize the environmental impacts of increased antibiotic use in human medicine and animal production, further research is essential to understand the effects of different antibiotics on plant physiology and productivity, uptake, translocation, and phytometabolism of antibiotics, and the role of antibiotics in the rhizosphere.
Collapse
Affiliation(s)
- Shiny Mathews
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48824, USA.
| | | |
Collapse
|
50
|
Poirel J, Joulian C, Leyval C, Billard P. Arsenite-induced changes in abundance and expression of arsenite transporter and arsenite oxidase genes of a soil microbial community. Res Microbiol 2013; 164:457-65. [DOI: 10.1016/j.resmic.2013.01.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 01/26/2013] [Indexed: 11/15/2022]
|