1
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Zhang Y, Wang Y, Han Y, Zhu S, Yan X. Impact of haze on potential pathogens in surface bioaerosol in urban environments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 355:124164. [PMID: 38754692 DOI: 10.1016/j.envpol.2024.124164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/18/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
Air quality considerably affects bioaerosol dynamics within the atmosphere. Frequent haze events, with their associated alterations in bioaerosol composition, may pose potential health risks. This study investigated the microbial diversity, community structure, and factors of PM2.5 within an urban environment. We further examined the impact of haze on potentially pathogenic bacteria in bioaerosols, and analyzed the sources of haze pollution. Key findings revealed that the highest levels of microbial richness and diversity were associated with lightly polluted air conditions. While the overall bacterial community structure remained relatively consistent across different air quality levels, the relative abundance of specific bacterial taxa exhibited variations. Meteorological and environmental conditions, particularly sulfur dioxide, nitrogen dioxide, and carbon monoxide, exerted a greater influence on bacterial diversity and community structure compared to the physicochemical properties of the PM2.5 particles themselves. Notably, haze events were observed to strengthen interactions among airborne pathogens. Stable carbon isotope analysis suggested that coal combustion and automobile exhaust were likely to represent the primary source of haze during winter months. These findings indicate that adoption of clean energy alternatives such as natural gas and electricity, and the use of public transportation, is crucial to mitigate particle and harmful pollutant emissions, thereby protecting public health.
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Affiliation(s)
- Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ying Wang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yunping Han
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Shuai Zhu
- School of Environment, Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Key Laboratory for Environmental Pollution Control, Henan Normal University, Xinxiang 453007, Henan, China.
| | - Xu Yan
- School of Environment, Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Key Laboratory for Environmental Pollution Control, Henan Normal University, Xinxiang 453007, Henan, China.
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2
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Hafezi Y, Omurzakov A, Carlisle JA, Caldas IV, Wolfner MF, Clark AG. The Drosophila melanogaster Y-linked gene, WDY, is required for sperm to swim in the female reproductive tract. Commun Biol 2024; 7:90. [PMID: 38216628 PMCID: PMC10786823 DOI: 10.1038/s42003-023-05717-x] [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: 03/20/2023] [Accepted: 12/18/2023] [Indexed: 01/14/2024] Open
Abstract
Unique patterns of inheritance and selection on Y chromosomes have led to the evolution of specialized gene functions. We report CRISPR mutants in Drosophila of the Y-linked gene, WDY, which is required for male fertility. We demonstrate that the sperm tails of WDY mutants beat approximately half as fast as those of wild-type and that mutant sperm do not propel themselves within the male ejaculatory duct or female reproductive tract. Therefore, although mature sperm are produced by WDY mutant males, and are transferred to females, those sperm fail to enter the female sperm storage organs. We report genotype-dependent and regional differences in sperm motility that appear to break the correlation between sperm tail beating and propulsion. Furthermore, we identify a significant change in hydrophobicity at a residue at a putative calcium-binding site in WDY orthologs at the split between the melanogaster and obscura species groups, when WDY first became Y-linked. This suggests that a major functional change in WDY coincided with its appearance on the Y chromosome. Finally, we show that mutants for another Y-linked gene, PRY, also show a sperm storage defect that may explain their subfertility. Overall, we provide direct evidence for the long-held presumption that protein-coding genes on the Drosophila Y regulate sperm motility.
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Affiliation(s)
- Yassi Hafezi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA.
| | - Arsen Omurzakov
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Jolie A Carlisle
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Ian V Caldas
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Mariana F Wolfner
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA.
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3
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Jiang HQ, Lu LY, Weng ZM, Huang KY, Yang Y, Deng HH, Xu YY, Chen W, Zhuang QQ. 6-Aza-2-Thiothymine-Capped Gold Nanoclusters as Robust Antimicrobial Nanoagents for Eradicating Multidrug-Resistant Escherichia coli Infection. ACS OMEGA 2023; 8:47123-47133. [PMID: 38107925 PMCID: PMC10720302 DOI: 10.1021/acsomega.3c07114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 11/14/2023] [Accepted: 11/20/2023] [Indexed: 12/19/2023]
Abstract
Multidrug-resistant bacterial infections, especially those caused by multidrug-resistant Escherichia coli (E. coli) bacteria, are an ever-growing threat because of the shrinking arsenal of efficacious antibiotics. Therefore, it is urgently needed to develop a kind of novel, long-term antibacterial agent effectively overcome resistant bacteria. Herein, we present a novel designed antibacterial agent-6-Aza-2-thiothymine-capped gold nanoclusters (ATT-AuNCs), which show excellent antibacterial activity against multidrug-resistant E. coli bacteria. The prepared AuNCs could permeabilize into the bacterial cell membrane via binding with a bivalent cation (e.g., Ca2+), followed by the generation of reactive oxygen species (e.g., •OH and •O2-), ultimately resulting in protein leakage from compromised cell membranes, inducing DNA damage and upregulating pro-oxidative genes intracellular. The AuNCs also speed up the wound healing process without noticeable hemolytic activity or cytotoxicity to erythrocytes and mammalian tissue. Altogether, the results indicate the great promise of ATT-AuNCs for treating multidrug-resistant E. coli bacterial infection.
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Affiliation(s)
- Hui-Qiong Jiang
- Department
of Cardiac Function Examination Room, Affiliated
Quanzhou First Hospital of Fujian Medical University, Quanzhou 362000, China
| | - Lin-Yan Lu
- Fujian
Key Laboratory of Drug Target Discovery and Structural and Functional
Research, School of Pharmacy, Fujian Medical
University, Fuzhou 350004, China
| | - Zhi-Min Weng
- Fujian
Key Laboratory of Drug Target Discovery and Structural and Functional
Research, School of Pharmacy, Fujian Medical
University, Fuzhou 350004, China
| | - Kai-Yuan Huang
- Fujian
Key Laboratory of Drug Target Discovery and Structural and Functional
Research, School of Pharmacy, Fujian Medical
University, Fuzhou 350004, China
| | - Yu Yang
- Fujian
Key Laboratory of Drug Target Discovery and Structural and Functional
Research, School of Pharmacy, Fujian Medical
University, Fuzhou 350004, China
| | - Hao-Hua Deng
- Fujian
Key Laboratory of Drug Target Discovery and Structural and Functional
Research, School of Pharmacy, Fujian Medical
University, Fuzhou 350004, China
| | - Ying-Ying Xu
- Department
of Pharmaceutics, School of Pharmacy, Fujian
Medical University, Fuzhou 350004, China
| | - Wei Chen
- Fujian
Key Laboratory of Drug Target Discovery and Structural and Functional
Research, School of Pharmacy, Fujian Medical
University, Fuzhou 350004, China
| | - Quan-Quan Zhuang
- Department
of Pharmacy, Affiliated Quanzhou First Hospital
of Fujian Medical University, Quanzhou 362000, China
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4
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Zuo W, Tian M, Qi J, Zhang G, Hu J, Wang S, Bao Y. The functions of EF-hand proteins from host and zoonotic pathogens. Microbes Infect 2023:105276. [PMID: 38072184 DOI: 10.1016/j.micinf.2023.105276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023]
Abstract
EF-hand proteins not only regulate biological processes, but also influence immunity and infection. In this review, we summarize EF-hand proteins' functions in host and zoonotic pathogens, with details in structures, Ca2+ affinity, downstream targets and functional mechanisms. Studies entitled as EF-hand-related but with less solid features were also discussed. We believe it could raise cautions and facilitate proper research strategy for researchers.
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Affiliation(s)
- Wei Zuo
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Mingxing Tian
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Jingjing Qi
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Guangdong Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Jiangang Hu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Shaohui Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; Engineering Research Center for the Prevention and Control of Animal Original Zoonosis of Fujian Province University, College of Life Science, Longyan University, Longyan, 364012, Fujian, China.
| | - Yanqing Bao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; Engineering Research Center for the Prevention and Control of Animal Original Zoonosis of Fujian Province University, College of Life Science, Longyan University, Longyan, 364012, Fujian, China.
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5
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Jung H, Su Z, Inaba Y, West AC, Banta S. Genetic Modification of Acidithiobacillus ferrooxidans for Rare-Earth Element Recovery under Acidic Conditions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:19902-19911. [PMID: 37983372 DOI: 10.1021/acs.est.3c05772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
As global demands for rare-earth elements (REEs) continue to grow, the biological recovery of REEs has been explored as a promising strategy, driven by potential economic and environmental benefits. It is known that calcium-binding domains, including helix-loop-helix EF hands and repeats-in-toxin (RTX) domains, can bind lanthanide ions due to their similar ionic radii and coordination preference to calcium. Recently, the lanmodulin protein from Methylorubrum extorquens was reported, which has evolved a high affinity for lanthanide ions over calcium. Acidithiobacillus ferrooxidans is a chemolithoautotrophic acidophile, which has been explored for use in bioleaching for metal recovery. In this report, A. ferrooxidans was engineered for the recombinant intracellular expression of lanmodulin. In addition, an RTX domain from the adenylate cyclase protein of Bordetella pertussis, which has previously been shown to bind Tb3+, was expressed periplasmically via fusion with the endogenous rusticyanin protein. The binding of lanthanides (Tb3+, Pr3+, Nd3+, and La3+) was improved by up to 4-fold for cells expressing lanmodulin and 13-fold for cells expressing the RTX domains in both pure and mixed metal solutions. Interestingly, the presence of lanthanides in the growth media enhanced protein expression, likely by influencing protein stability. Both engineered cell lines exhibited higher recoveries and selectivities for four tested lanthanides (Tb3+, Pr3+, Nd3+, and La3+) over non-REEs (Fe2+ and Co2+) in a synthetic magnet leachate, demonstrating the potential of these new strains for future REE reclamation and recycling applications.
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Affiliation(s)
- Heejung Jung
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, New York 10027, United States
| | - Zihang Su
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, New York 10027, United States
| | - Yuta Inaba
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, New York 10027, United States
| | - Alan C West
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, New York 10027, United States
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, New York 10027, United States
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6
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Agaras BC, Grossi CEM, Ulloa RM. Unveiling the Secrets of Calcium-Dependent Proteins in Plant Growth-Promoting Rhizobacteria: An Abundance of Discoveries Awaits. PLANTS (BASEL, SWITZERLAND) 2023; 12:3398. [PMID: 37836138 PMCID: PMC10574481 DOI: 10.3390/plants12193398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023]
Abstract
The role of Calcium ions (Ca2+) is extensively documented and comprehensively understood in eukaryotic organisms. Nevertheless, emerging insights, primarily derived from studies on human pathogenic bacteria, suggest that this ion also plays a pivotal role in prokaryotes. In this review, our primary focus will be on unraveling the intricate Ca2+ toolkit within prokaryotic organisms, with particular emphasis on its implications for plant growth-promoting rhizobacteria (PGPR). We undertook an in silico exploration to pinpoint and identify some of the proteins described in the existing literature, including prokaryotic Ca2+ channels, pumps, and exchangers that are responsible for regulating intracellular Calcium concentration ([Ca2+]i), along with the Calcium-binding proteins (CaBPs) that play a pivotal role in sensing and transducing this essential cation. These investigations were conducted in four distinct PGPR strains: Pseudomonas chlororaphis subsp. aurantiaca SMMP3, P. donghuensis SVBP6, Pseudomonas sp. BP01, and Methylobacterium sp. 2A, which have been isolated and characterized within our research laboratories. We also present preliminary experimental data to evaluate the influence of exogenous Ca2+ concentrations ([Ca2+]ex) on the growth dynamics of these strains.
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Affiliation(s)
- Betina Cecilia Agaras
- Laboratory of Physiology and Genetics of Plant Probiotic Bacteria (LFGBBP), Centre of Biochemistry and Microbiology of Soils, National University of Quilmes, Bernal B1876BXD, Argentina
- National Scientific and Technical Research Council (CONICET), Buenos Aires C1425FQB, Argentina;
| | - Cecilia Eugenia María Grossi
- National Scientific and Technical Research Council (CONICET), Buenos Aires C1425FQB, Argentina;
- Laboratory of Plant Signal Transduction, Institute of Genetic Engineering and Molecular Biology (INGEBI), National Scientific and Technical Research Council (CONICET), Buenos Aires C1425FQB, Argentina
| | - Rita María Ulloa
- National Scientific and Technical Research Council (CONICET), Buenos Aires C1425FQB, Argentina;
- Laboratory of Plant Signal Transduction, Institute of Genetic Engineering and Molecular Biology (INGEBI), National Scientific and Technical Research Council (CONICET), Buenos Aires C1425FQB, Argentina
- Biochemistry Department, Faculty of Exact and Natural Sciences, University of Buenos Aires (FCEN-UBA), Buenos Aires C1428EGA, Argentina
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7
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Ryder S, Pedigo J, Ojennus DD. Elucidating the Role of a Calcium-Binding Loop in an x-Prolyl Aminodipeptidase from Lb. helveticus. ACS OMEGA 2023; 8:35410-35416. [PMID: 37779945 PMCID: PMC10536834 DOI: 10.1021/acsomega.3c05639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/31/2023] [Indexed: 10/03/2023]
Abstract
Prolyl aminodipeptidase (PepX) is an α/β hydrolase that cleaves at penultimate N-terminal prolyl peptide bonds. The crystal structure of PepX from Lactobacillus helveticus exhibits a calcium-binding loop within the catalytic domain. The calcium-binding sequence of xDxDxDGxxD within this loop is highly conserved in PepX proteins among lactic acid bacteria, but its purpose remains unknown. Enzyme activity is not significantly affected in the presence of the metal chelator ethylenediaminetetraacetic acid (EDTA), nor in the presence of excess calcium ions. To eliminate calcium binding, D196A and D194A/D196A mutations were constructed within the conserved calcium-binding sequence motif. Enzyme activity and stability of the D196A mutant were comparable to the wild-type enzyme by colorimetric kinetic assays and protein thermal shift assays. However, the D194A/D196A mutant was inactive though it retained native-like structure and thermal stability, contradicting the EDTA and calcium titration results. This suggests calcium binding to PepX may be essential for activity.
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Affiliation(s)
- Stephanie Ryder
- Department of Chemistry, Whitworth
University, 300 W. Hawthorne Rd., Spokane, Washington 99251, United States
| | | | - Deanna Dahlke Ojennus
- Department of Chemistry, Whitworth
University, 300 W. Hawthorne Rd., Spokane, Washington 99251, United States
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8
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Arabi D, Hamdy O, Mohamed MSM, Abdel-Salam Z, Abdel-Harith M. Discriminating two bacteria via laser-induced breakdown spectroscopy and artificial neural network. AMB Express 2023; 13:61. [PMID: 37338621 DOI: 10.1186/s13568-023-01569-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 06/06/2023] [Indexed: 06/21/2023] Open
Abstract
Rapid and successful clinical diagnosis and bacterial infection treatment depend on accurate identification and differentiation between different pathogenic bacterial species. A lot of efforts have been made to utilize modern techniques which avoid the laborious work and time-consuming of conventional methods to fulfill this task. Among such techniques, laser-induced breakdown spectroscopy (LIBS) can tell much about bacterial identity and functionality. In the present study, a sensitivity-improved version of LIBS, i.e. nano-enhanced LIBS (NELIBS), has been used to discriminate between two different bacteria (Pseudomonas aeruginosa and Proteus mirabilis) belonging to different taxonomic orders. Biogenic silver nanoparticles (AgNPs) are sprinkled onto the samples' surface to have better discrimination capability of the technique. The obtained spectroscopic results of the NELIBS approach revealed superior differentiation between the two bacterial species compared to the results of the conventional LIBS. Identification of each bacterial species has been achieved in light of the presence of spectral lines of certain elements. On the other hand, the discrimination was successful by comparing the intensity of the spectral lines in the spectra of the two bacteria. In addition, an artificial neural network (ANN) model has been created to assess the variation between the two data sets, affecting the differentiation process. The results revealed that NELIBS provides higher sensitivity and more intense spectral lines with increased detectable elements. The ANN results showed that the accuracy rates are 88% and 92% for LIBS and NELIBS, respectively. In the present work, it has been demonstrated that NELIBS combined with ANN successfully differentiated between both bacteria rapidly with high precision compared to conventional microbiological discrimination techniques and with minimum sample preparation.
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Affiliation(s)
- Dina Arabi
- Laser Applications in Metrology, Photochemistry and Agriculture Department, National Institute of Laser Enhanced Science, Cairo University, Giza, 12613, Egypt
| | - Omnia Hamdy
- Engineering Applications of Lasers Department, National Institute of Laser Enhanced Science, Cairo University, Giza, 12613, Egypt
| | - Mahmoud S M Mohamed
- Botany and Microbiology Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Zienab Abdel-Salam
- Laser Applications in Metrology, Photochemistry and Agriculture Department, National Institute of Laser Enhanced Science, Cairo University, Giza, 12613, Egypt
| | - Mohamed Abdel-Harith
- Laser Applications in Metrology, Photochemistry and Agriculture Department, National Institute of Laser Enhanced Science, Cairo University, Giza, 12613, Egypt.
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9
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Pan Z, Fan L, Zhong Y, Guo J, Dong X, Xu X, Wang C, Su Y. Quantitative proteomics reveals reduction in central carbon and energy metabolisms contributes to gentamicin resistance in Staphylococcus aureus. J Proteomics 2023; 277:104849. [PMID: 36809838 DOI: 10.1016/j.jprot.2023.104849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/11/2023] [Accepted: 02/12/2023] [Indexed: 02/22/2023]
Abstract
The emergence of antibiotic resistance greatly increases the difficulty of treating bacterial infections. In order to develop effective treatments, the underlying mechanisms of antibiotic resistance must be understood. In this study, Staphylococcus aureus ATCC6538 strain was passaged in medium with and without gentamicin and obtained lab-evolved gentamicin-resistant S. aureus (RGEN) and gentamicin-sensitive S. aureus (SGEN) strains, respectively. Data-Independent Acquisition (DIA)-based proteomics approach was applied to compare the two strains. A total of 1426 proteins were identified, of which 462 were significantly different: 126 were upregulated and 336 were downregulated in RGEN compared to SGEN. Further analysis found that reduced protein biosynthesis was a characteristic feature in RGEN, related to metabolic suppression. The most differentially expressed proteins were involved in metabolic pathways. In RGEN, central carbon metabolism was dysregulated and energy metabolism decreased. After verification, it was found that the levels of NADH, ATP, and reactive oxygen species (ROS) decreased, and superoxide dismutase and catalase activities increased. These findings suggest that inhibition of central carbon and energy metabolic pathways may play an important role in the resistance of S. aureus to gentamicin, and that gentamicin resistance is associated with oxidative stress. Significance: The overuse and misuse of antibiotics have led to bacterial antibiotic resistance, which is a serious threat to human health. Understanding the mechanisms of antibiotic resistance will help better control these antibiotic-resistant pathogens in the future. The present study characterized the differential proteome of gentamicin-resistant Staphylococcus aureus using the most advanced DIA-based proteomics technology. Many of the differential expressed proteins were related to metabolism, specifically, reduced central carbon and energy metabolism. Lower levels of NADH, ROS, and ATP were detected as a consequence of the reduced metabolism. These results reveal that downregulation of protein expression affecting central carbon and energy metabolisms may play an important role in the resistance of S. aureus to gentamicin.
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Affiliation(s)
- Zhiyu Pan
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Lvyuan Fan
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yilin Zhong
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Juan Guo
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xuesa Dong
- Shandong Freshwater Fisheries Research Institute, Jinan 250013, China
| | - Xiao Xu
- Shandong Freshwater Fisheries Research Institute, Jinan 250013, China
| | - Chao Wang
- Shandong Freshwater Fisheries Research Institute, Jinan 250013, China.
| | - Yubin Su
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
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10
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Hafezi Y, Omurzakov A, Carlisle JA, Caldas IV, Wolfner MF, Clark AG. The Drosophila melanogaster Y-linked gene, WDY, is required for sperm to swim in the female reproductive tract. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.02.526876. [PMID: 36778485 PMCID: PMC9915733 DOI: 10.1101/2023.02.02.526876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Unique patterns of inheritance and selection on Y chromosomes lead to the evolution of specialized gene functions. Yet characterizing the function of genes on Y chromosomes is notoriously difficult. We report CRISPR mutants in Drosophila of the Y-linked gene, WDY, which is required for male fertility. WDY mutants produce mature sperm with beating tails that can be transferred to females but fail to enter the female sperm storage organs. We demonstrate that the sperm tails of WDY mutants beat approximately half as fast as wild-type sperm's and that the mutant sperm do not propel themselves within the male ejaculatory duct or female reproductive tract (RT). These specific motility defects likely cause the sperm storage defect and sterility of the mutants. Regional and genotype-dependent differences in sperm motility suggest that sperm tail beating and propulsion do not always correlate. Furthermore, we find significant differences in the hydrophobicity of key residues of a putative calcium-binding domain between orthologs of WDY that are Y-linked and those that are autosomal. Given that WDY appears to be evolving under positive selection, our results suggest that WDY's functional evolution coincides with its transition from autosomal to Y-linked in Drosophila melanogaster and its most closely related species. Finally, we show that mutants for another Y-linked gene, PRY, also show a sperm storage defect that may explain their subfertility. In contrast to WDY, PRY mutants do swim in the female RT, suggesting they are defective in yet another mode of motility, navigation, or a necessary interaction with the female RT. Overall, we provide direct evidence for the long-held presumption that protein-coding genes on the Drosophila Y regulate sperm motility.
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11
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Discovery and Mechanism of Action of a Novel Antimicrobial Peptide from an Earthworm. Microbiol Spectr 2023; 11:e0320622. [PMID: 36602379 PMCID: PMC9927515 DOI: 10.1128/spectrum.03206-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The robust innate immune system of the earthworm provides a potential source of natural antimicrobial peptides (AMPs). However, the cost and high rediscovery rate of direct separation and purification limits their discovery. Genome sequencing of numerous earthworm species facilitates the discovery of new antimicrobial peptides. Through predicting potential antimicrobial peptides in the open reading frames of the Eisenia andrei genome and sequence optimization, a novel antimicrobial peptide, named EWAMP-R (RIWWSGGWRRWRW), was identified. EWAMP-R demonstrated good activity against various bacteria, including drug-resistant strains. The antibacterial mechanisms of EWAMP-R were explored through molecular simulation and wet-laboratory experiments. These experiments demonstrated that the bacterial membrane may be one of the targets of EWAMP-R but that there may be different interactions with Gram-negative and Gram-positive bacterial membranes. EWAMP-R can disrupt bacterial membrane integrity; however, at low concentrations, it appears that EWAMP-R may get through the membrane of Escherichia coli instead of damaging it directly, implying the existence of a secondary response. Gene expression studies identified that in E. coli, only the apoptosis-like cell death (ALD) pathway was activated, while in Staphylococcus aureus, the MazEF pathway was also upregulated, limiting the influence of the ALD pathway. The different antimicrobial actions against Gram-positive and -negative bacteria can provide important information on the structure-activity relationship of AMPs and facilitate AMP design with higher specificity. This study identified a new source of antibacterial agents that has the potential to address the increasingly serious issue of antibiotic resistance. IMPORTANCE Drug-resistant bacteria are a great threat to public health and drive the search for new antibacterial agents. The living environment of earthworms necessitates a strong immune system, and therefore, they are potentially a rich resource of novel antibiotics. A novel AMP, EWAMP-R, with high antibacterial activity was found through in silico analysis of the Eisenia andrei genome. Molecular analysis investigating the interactions between EWAMP-R and the cell membrane demonstrated the importance of tryptophan and arginine residues to EWAMP-R activity. Additionally, the different secondary responses found between E. coli and S. aureus were in accordance with a common phenomenon where some antibacterial agents only target specific species of bacteria. These results provided useful molecular information to support further AMP research and design. Our study expands the sources of antimicrobial peptides and also helps to explain the adaptability of earthworms to their environment.
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12
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Calmodulin in Paramecium: Focus on Genomic Data. Microorganisms 2022; 10:microorganisms10101915. [PMID: 36296191 PMCID: PMC9608856 DOI: 10.3390/microorganisms10101915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/14/2022] [Accepted: 09/22/2022] [Indexed: 11/26/2022] Open
Abstract
Calcium (Ca2+) is a universal second messenger that plays a key role in cellular signaling. However, Ca2+ signals are transduced with the help of Ca2+-binding proteins, which serve as sensors, transducers, and elicitors. Among the collection of these Ca2+-binding proteins, calmodulin (CaM) emerged as the prototypical model in eukaryotic cells. This is a small protein that binds four Ca2+ ions and whose functions are multiple, controlling many essential aspects of cell physiology. CaM is universally distributed in eukaryotes, from multicellular organisms, such as human and land plants, to unicellular microorganisms, such as yeasts and ciliates. Here, we review most of the information gathered on CaM in Paramecium, a group of ciliates. We condense the information here by mentioning that mature Paramecium CaM is a 148 amino acid-long protein codified by a single gene, as in other eukaryotic microorganisms. In these ciliates, the protein is notoriously localized and regulates cilia function and can stimulate the activity of some enzymes. When Paramecium CaM is mutated, cells show flawed locomotion and/or exocytosis. We further widen this and additional information in the text, focusing on genomic data.
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Yang L, Shen Z, Wei J, Wang X, Xu H, Sun J, Wang Q, Cao J. Size distribution, community composition, and influencing factors of bioaerosols on haze and non-haze days in a megacity in Northwest China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:155969. [PMID: 35588847 DOI: 10.1016/j.scitotenv.2022.155969] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 04/20/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Bioaerosols have become a major environmental concern in recent years. In this study, the diurnal variations and size distributions of bioaerosols, as well as airborne bacterial community compositions and their influencing factors on haze and non-haze days in Xi'an, China, were compared. The results indicated that the mean bacteria and fungi concentrations on non-haze days were 1.7 and 1.4 times of those on haze days, respectively, whereas the mean total airborne microbe (TAM) concentration was higher on haze days. Bacteria concentrations were the lowest in the afternoon, and the TAM concentration exhibited a bimodal distribution with two peaks coinciding with traffic rush hours. On haze days airborne fungi was mainly attached to PM2.5, whereas bacteria and TAM were mainly distributed in coarse PM. The relative abundance of Chao1, Shannon and Simpson indices of bacterial communities were higher in the non-haze day samples, for the reason that high PM2.5 levels with a large specific surface area may absorb more toxic and harmful substances on haze days, which should affect microbial growth. At the generic level, the relative abundance of Rhodococcus, Paracoccus, Acinetobacter, and Kocuria on haze days was higher than that on non-haze days, indicating a higher risk of contracting pathogenic pneumonia. The results of the redundancy analysis revealed that PM2.5 and water-soluble inorganic ions (WSIIs, NO3-, SO42+, and NH4+) strongly affected the bacterial communities on non-haze days, especially Acinetobacter. The atmospheric oxidation capacity (Ox) had a significant effect on bacterial communities during haze episodes, which were positively correlated with Paracoccus, Deinococcus, Sphingomonas, and Rubellimicrobium and were negatively correlated with Rhodococcus. These results provide valuable data to elucidate the formation and evolution of bioaerosol between haze and non-haze events and its potential threats to human health.
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Affiliation(s)
- Liu Yang
- Department of Environmental Science and Engineering, Xi'an Jiaotong University, Xi'an 710049, China; Key Lab of Aerosol Chemistry & Physics, SKLLQG, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710049, China
| | - Zhenxing Shen
- Department of Environmental Science and Engineering, Xi'an Jiaotong University, Xi'an 710049, China; Key Lab of Aerosol Chemistry & Physics, SKLLQG, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710049, China.
| | - Junqiang Wei
- Department of Environmental Science and Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Xiuru Wang
- Department of Environmental Science and Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Hongmei Xu
- Department of Environmental Science and Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Jian Sun
- Department of Environmental Science and Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Qiyuan Wang
- Key Lab of Aerosol Chemistry & Physics, SKLLQG, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710049, China
| | - Junji Cao
- Key Lab of Aerosol Chemistry & Physics, SKLLQG, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710049, China
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14
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Beirne C, McCann E, McDowell A, Miliotis G. Genetic determinants of antimicrobial resistance in three multi-drug resistant strains of Cutibacterium acnes isolated from patients with acne: a predictive in silico study. Access Microbiol 2022; 4:acmi000404. [PMID: 36133174 PMCID: PMC9484663 DOI: 10.1099/acmi.0.000404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 07/06/2022] [Indexed: 01/09/2023] Open
Abstract
Objectives. Using available whole genome data, the objective of this in silico study was to identify genetic mechanisms that could explain the antimicrobial resistance profile of three multi-drug resistant (MDR) strains (CA17, CA51, CA39) of the skin bacterium
Cutibacterium acnes
previously recovered from patients with acne. In particular, we were interested in detecting novel genetic determinants associated with resistance to fluoroquinolone and macrolide antibiotics that could then be confirmed experimentally.
Methods. A range of open source bioinformatics tools were used to ‘mine’ genetic determinants of antimicrobial resistance and plasmid borne contigs, and to characterise the phylogenetic diversity of the MDR strains.
Results. As probable mechanisms of resistance to fluoroquinolones, we identified a previously described resistance associated allelic variant of the gyrA gene with a ‘deleterious' S101L mutation in type IA1 strains CA51 (ST1) and CA39 (ST1), as well as a novel E761R ‘deleterious’ mutation in the type II strain CA17 (ST153). A distinct genomic sequence of the efflux protein YfmO which is potentially associated with resistance to MLSB antibiotics was also present in CA17; homologues in CA51, CA39, and other strains of
Cutibacterium acnes
, were also found but differed in amino acid content. Strikingly, in CA17 we also identified a circular 2.7 kb non-conjugative plasmid (designated pCA17) that closely resembled a 4.8 kb plasmid (pYU39) from the MDR
Salmonella enterica
strain YU39.
Conclusions. This study has provided a detailed explanation of potential genetic determinants for MDR in the
Cutibacterium acnes
strains CA17, CA39 and CA51. Further laboratory investigations will be required to validate these in silico results, especially in relation to pCA17.
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Affiliation(s)
- Catriona Beirne
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland
| | - Emily McCann
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland
| | - Andrew McDowell
- Nutrition Innovation Centre for Food and Health, (NICHE), School of Biomedical Sciences, Ulster University, Coleraine, Ireland
| | - Georgios Miliotis
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland
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Méheust R, Castelle CJ, Jaffe AL, Banfield JF. Conserved and lineage-specific hypothetical proteins may have played a central role in the rise and diversification of major archaeal groups. BMC Biol 2022; 20:154. [PMID: 35790962 PMCID: PMC9258230 DOI: 10.1186/s12915-022-01348-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Archaea play fundamental roles in the environment, for example by methane production and consumption, ammonia oxidation, protein degradation, carbon compound turnover, and sulfur compound transformations. Recent genomic analyses have profoundly reshaped our understanding of the distribution and functionalities of Archaea and their roles in eukaryotic evolution. RESULTS Here, 1179 representative genomes were selected from 3197 archaeal genomes. The representative genomes clustered based on the content of 10,866 newly defined archaeal protein families (that will serve as a community resource) recapitulates archaeal phylogeny. We identified the co-occurring proteins that distinguish the major lineages. Those with metabolic roles were consistent with experimental data. However, two families specific to Asgard were determined to be new eukaryotic signature proteins. Overall, the blocks of lineage-specific families are dominated by proteins that lack functional predictions. CONCLUSIONS Given that these hypothetical proteins are near ubiquitous within major archaeal groups, we propose that they were important in the origin of most of the major archaeal lineages. Interestingly, although there were clearly phylum-specific co-occurring proteins, no such blocks of protein families were shared across superphyla, suggesting a burst-like origin of new lineages early in archaeal evolution.
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Affiliation(s)
- Raphaël Méheust
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA. .,Innovative Genomics Institute, University of California, Berkeley, CA, USA. .,LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, Evry, France.
| | - Cindy J Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Alexander L Jaffe
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA. .,Innovative Genomics Institute, University of California, Berkeley, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA. .,Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA.
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16
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Choo M, Oh S, Jo S, Jin X, Song Y, Wen H, Park S, Kang S. Highly conserved protein Rv1211 in Mycobacterium tuberculosis is a natively unfolded protein that binds to a calmodulin antagonist, trifluoperazine. Biochem Biophys Res Commun 2022; 610:182-187. [PMID: 35468422 DOI: 10.1016/j.bbrc.2022.04.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 04/10/2022] [Indexed: 11/02/2022]
Abstract
Rv1211 is a conserved hypothetical protein in Mycobacterium tuberculosis and is required for the growth and pathogenesis of the bacteria. The protein has been suggested as a calmodulin-like calcium-binding protein with an EF-hand motif and as a target of trifluoperazine, a calmodulin antagonist in eukaryotes that inhibits mycobacterial growth. Here, we expressed the recombinant protein of Rv1211 and performed structural and biochemical studies of Rv1211 and its interaction with Ca2+ or trifluoperazine. Surprisingly, Rv1211 exhibited an elution property typical of a natively unfolded protein. Subsequent circular dichroism experiments with temperature elevation and trifluoroethanol treatment showed that Rv1211 has unfolded structure. Additional NMR experiment confirmed the unfolded state of the protein and further showed that it does not bind to Ca2+. Still, Rv1211 did bind to trifluoperazine, as evidenced by the two-dimensional NMR spectra of 15N-labeled Rv1211. However, there were no peak shifts upon binding, showing that Rv1211 retained its unfolded state even after the trifluoperazine binding. The residues involved in the binding were clustered in the C-terminal region, as identified by the sequence assignment. Isothermal titration calorimetry showed that the Kd of trifluoperazine-Rv1211 binding is 41 μM and that the stoichiometry is 1 : 2 (Rv1211: trifluoperazine). Our results argue against the suggestion of Rv1211 as a Ca2+-binding calmodulin-like protein, and show that Rv1211 is a natively unfolded protein that binds to trifluoperazine. In addition, our results suggest the evidence of the "Fuzziness" in the Rv1211-trifluoperazine interaction that differs from the conventional binding-induced folding of natively unfolded proteins.
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Affiliation(s)
- Munki Choo
- Natural Product Research Institute, College of Pharmacy, Seoul National University, Gwanak-Ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Sehyun Oh
- Natural Product Research Institute, College of Pharmacy, Seoul National University, Gwanak-Ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Sihyang Jo
- Natural Product Research Institute, College of Pharmacy, Seoul National University, Gwanak-Ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Xing Jin
- Natural Product Research Institute, College of Pharmacy, Seoul National University, Gwanak-Ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Yonghyun Song
- Department of Biochemistry, Inha University Hospital, College of Medicine, Inha University, Incheon, 22212, Republic of Korea
| | - He Wen
- Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Sunghyouk Park
- Natural Product Research Institute, College of Pharmacy, Seoul National University, Gwanak-Ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea.
| | - Sunmi Kang
- Natural Product Research Institute, College of Pharmacy, Seoul National University, Gwanak-Ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea.
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17
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Pengelly RJ, Bakhtiar D, Borovská I, Královičová J, Vořechovský I. Exonic splicing code and protein binding sites for calcium. Nucleic Acids Res 2022; 50:5493-5512. [PMID: 35474482 PMCID: PMC9177970 DOI: 10.1093/nar/gkac270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/01/2022] [Accepted: 04/05/2022] [Indexed: 11/12/2022] Open
Abstract
Auxilliary splicing sequences in exons, known as enhancers (ESEs) and silencers (ESSs), have been subject to strong selection pressures at the RNA and protein level. The protein component of this splicing code is substantial, recently estimated at ∼50% of the total information within ESEs, but remains poorly understood. The ESE/ESS profiles were previously associated with the Irving-Williams (I-W) stability series for divalent metals, suggesting that the ESE/ESS evolution was shaped by metal binding sites. Here, we have examined splicing activities of exonic sequences that encode protein binding sites for Ca2+, a weak binder in the I-W affinity order. We found that predicted exon inclusion levels for the EF-hand motifs and for Ca2+-binding residues in nonEF-hand proteins were higher than for average exons. For canonical EF-hands, the increase was centred on the EF-hand chelation loop and, in particular, on Ca2+-coordinating residues, with a 1>12>3∼5>9 hierarchy in the 12-codon loop consensus and usage bias at codons 1 and 12. The same hierarchy but a lower increase was observed for noncanonical EF-hands, except for S100 proteins. EF-hand loops preferentially accumulated exon splits in two clusters, one located in their N-terminal halves and the other around codon 12. Using splicing assays and published crosslinking and immunoprecipitation data, we identify candidate trans-acting factors that preferentially bind conserved GA-rich motifs encoding negatively charged amino acids in the loops. Together, these data provide evidence for the high capacity of codons for Ca2+-coordinating residues to be retained in mature transcripts, facilitating their exon-level expansion during eukaryotic evolution.
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Affiliation(s)
- Reuben J Pengelly
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Dara Bakhtiar
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Ivana Borovská
- Slovak Academy of Sciences, Centre of Biosciences, 840 05 Bratislava, Slovak Republic
| | - Jana Královičová
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
- Slovak Academy of Sciences, Centre of Biosciences, 840 05 Bratislava, Slovak Republic
- Slovak Academy of Sciences, Institute of Zoology, 845 06 Bratislava, Slovak Republic
| | - Igor Vořechovský
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
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Zhang Q, Cheng YF, Huang BC, Jin RC. A review of heavy metals inhibitory effects in the process of anaerobic ammonium oxidation. JOURNAL OF HAZARDOUS MATERIALS 2022; 429:128362. [PMID: 35121298 DOI: 10.1016/j.jhazmat.2022.128362] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/15/2022] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Anaerobic ammonium oxidation (anammox) is a promising biological technology for treating ammonium-rich wastewaters. However, due to the high sensitivity of anammox bacteria, many external factors have inhibitory effects on this process. As one of the commonly found toxic substances in wastewater, heavy metals (HMs) are possible to cause inhibition on anammox sludge, which then results in a declined treatment performance. Getting insights into the response mechanism of anammox sludge to HMs is meaningful for its application in treating this kind of wastewater. This review summarized the effect of different HMs on treatment performance of anammox bioreactor. In addition, the mechanism of toxication raised by HMs was discussed. Also, the potential mitigation strategies were summarized and the future prospects were outlooked. This review might provide useful information for both scientific research on and engineering application of anammox process for treating HMs containing wastewater.
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Affiliation(s)
- Qian Zhang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Ya-Fei Cheng
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Bao-Cheng Huang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Ren-Cun Jin
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China.
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He T, Chen M, Ding C, Wu Q, Zhang M. Hypothermia Pseudomonas taiwanensis J488 exhibited strong tolerance capacity to high dosages of divalent metal ions during nitrogen removal process. BIORESOURCE TECHNOLOGY 2021; 341:125785. [PMID: 34455248 DOI: 10.1016/j.biortech.2021.125785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
The nitrogen metabolic pathways of Pseudomonas taiwanensis J488 have not been confirmed from genomic function analysis and its divalent metal ion resistance remains poorly understood. In this study, the key denitrifying gene of Pseudomonas taiwanensis J488, nirB, was determined by draft genome sequencing. The nitrification of ammonium was insensitive to high concentrations of Ca(II), Mn(II), Zn(II), and Cd(II). Similarly, complete nitrite removal was achieved despite Mn(II) and Zn(II) reaching concentrations up to 30 mg/L. Furthermore, the efficiency of nitrate removal was significantly enhanced by 1.33%, 3.33%, 5.99%, and 1.53% with the addition of 0.5 mg/L Ca(II), 20 mg/L Mn(II), 5 mg/L Zn(II), and 2 mg/L Cd(II), respectively, comparison with the control. The bacterial growth in both nitrifying and denitrifying processes was substantially promoted by various dosages of divalent metal ions. These results indicate that divalent metal ions would not severely limit the capacity of strain J488 to purify nitrogen-polluted wastewater.
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Affiliation(s)
- Tengxia He
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China.
| | - Mengping Chen
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China
| | - Chenyu Ding
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China
| | - Qifeng Wu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China
| | - Manman Zhang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China
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20
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Fathollahi A, Coupe SJ. Effect of environmental and nutritional conditions on the formation of single and mixed-species biofilms and their efficiency in cadmium removal. CHEMOSPHERE 2021; 283:131152. [PMID: 34147985 DOI: 10.1016/j.chemosphere.2021.131152] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/29/2021] [Accepted: 06/05/2021] [Indexed: 06/12/2023]
Abstract
Remediation of contaminated water and wastewater using biosorption methods has attracted significant attention in recent decades due to its efficiency, convenience and minimised environmental effects. Bacterial biosorbents are normally deployed as a non-living powder or suspension. Little is known about the mechanisms or rates of bacterial attachment to surfaces and effect of various conditions on the biofilm development, as well as efficiency of living biofilms in the removal of heavy metals. In the present study, the effect of environmental and nutritional conditions such as pH, temperature, concentrations of phosphate, glucose, amino acid, nitrate, calcium and magnesium, on planktonic and biofilm growth of single and mixed bacterial cultures, were measured. Actinomyces meyeri, Bacillus cereus, Escherichia coli, Pseudomonas fluorescens strains were evaluated to determine the optimum biofilm growth conditions. The Cd(II) biosorption efficiencies of the mixed-species biofilm developed in the optimum growth condition, were investigated and modelled using Langmuir, Freundlich and Dubnin Radushkevich models. The biofilm quantification techniques revealed that the optimum concentration of phosphate, glucose, amino acid, nitrate, calcium and magnesium for the biofilm development were 25, 10, 1, 1.5, 5 and 0.5 g L-1, respectively. Further increases in the nutrient concentrations resulted in less biofilm growth. The optimum pH for the biofilm growth was 7 and alkaline or acidic conditions caused significant negative effects on the bacterial attachment and development. The optimum temperatures for the bacterial attachment to the surface were between 25 and 35 °C. The maximum Cd(II) biosorption efficiency (99%) and capacity (18.19 mg g-1) of the mixed-species biofilm, occurred on day 35 (Ci = 0.1 mg L-1) and 1 (Ci = 20 mg L-1) of biofilm growth, respectively. Modelling of the biosorption data revealed that Cd(II) removal by the living biofilm was a physical process by a monolayer of biofilm. The results of present study suggested that environmental and nutritional conditions had a significant effect on bacterial biofilm formation and its efficiency in Cd(II) removal.
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Affiliation(s)
- Alireza Fathollahi
- Centre for Agroecology Water and Resilience (CAWR), Coventry University, Wolston Lane, Ryton on Dunsmore, CV8 3LG, UK.
| | - Stephen J Coupe
- Centre for Agroecology Water and Resilience (CAWR), Coventry University, Wolston Lane, Ryton on Dunsmore, CV8 3LG, UK
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21
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Hemkemeyer M, Schwalb SA, Heinze S, Joergensen RG, Wichern F. Functions of elements in soil microorganisms. Microbiol Res 2021; 252:126832. [PMID: 34508963 DOI: 10.1016/j.micres.2021.126832] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022]
Abstract
The soil microbial community fulfils various functions, such as nutrient cycling and carbon (C) sequestration, therefore contributing to maintenance of soil fertility and mitigation of global warming. In this context, a major focus of research has been on C, nitrogen (N) and phosphorus (P) cycling. However, from aquatic and other environments, it is well known that other elements beyond C, N, and P are essential for microbial functioning. Nonetheless, for soil microorganisms this knowledge has not yet been synthesised. To gain a better mechanistic understanding of microbial processes in soil systems, we aimed at summarising the current knowledge on the function of a range of essential or beneficial elements, which may affect the efficiency of microbial processes in soil. This knowledge is discussed in the context of microbial driven nutrient and C cycling. Our findings may support future investigations and data evaluation, where other elements than C, N, and P affect microbial processes.
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Affiliation(s)
- Michael Hemkemeyer
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany.
| | - Sanja A Schwalb
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany
| | - Stefanie Heinze
- Department of Soil Science & Soil Ecology, Ruhr-University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Rainer Georg Joergensen
- Department of Soil Biology and Plant Nutrition, University of Kassel, Nordbahnhofstr. 1a, 37213 Witzenhausen, Germany
| | - Florian Wichern
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany
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22
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Xie Z, Du S, Ma T, Hou J, Zeng X, Li Y. High time-resolved characterization of airborne microbial community during a typical haze pollution process. JOURNAL OF HAZARDOUS MATERIALS 2021; 415:125722. [PMID: 34088212 DOI: 10.1016/j.jhazmat.2021.125722] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/04/2021] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Abstract
Variations of bioaerosol characteristics during the process of haze pollution have rarely been explored. In this study, high time-resolved variations of the community structures of bacteria, fungi, and ammonia-oxidizing microorganisms (AOMs) were assessed during a typical haze pollution process. The impacts of meteorological factors, water-soluble inorganic ions (WSII), and organic dicarboxylic acids (DCA) on the airborne microbial community were systematically evaluated. The results showed that the bacterial community varied greatly during the formation stages of haze pollution, and tended to stabilize with the further development of haze pollution. Nevertheless, variations of the fungal community lasted throughout the whole haze pollution process. Furthermore, Nitrososphaera absolutely dominated the ammonia-oxidizing archaea (AOA) and declined as PM2.5 burst. Network analysis identified relatively weak interactions and co-occurrence patterns between dominant fungal genera. Importantly, dust source ions and PM2.5 acidity exerted the most significant impacts on bacterial and fungal communities. These results identify the high time-resolved variations of airborne microbial communities during the formation and development of haze pollution process, and provide valuable data to better understand the interaction between bioaerosols and haze pollution.
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Affiliation(s)
- Zhengsheng Xie
- School of Water and Environment, Chang'an University, Xi'an 710054, China.
| | - Shengli Du
- School of Water and Environment, Chang'an University, Xi'an 710054, China
| | - Tianfeng Ma
- School of Water and Environment, Chang'an University, Xi'an 710054, China
| | - Junli Hou
- School of Water and Environment, Chang'an University, Xi'an 710054, China
| | - Xuelin Zeng
- School of Water and Environment, Chang'an University, Xi'an 710054, China
| | - Yanpeng Li
- School of Water and Environment, Chang'an University, Xi'an 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region (Chang'an University), Ministry of Education, Xi'an 710054, China.
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Sun X, Li D, Li B, Sun S, Yabo SD, Geng J, Ma L, Qi H. Exploring the disparity of inhalable bacterial communities and antibiotic resistance genes between hazy days and non-hazy days in a cold megacity in Northeast China. JOURNAL OF HAZARDOUS MATERIALS 2020; 398:122984. [PMID: 32512457 DOI: 10.1016/j.jhazmat.2020.122984] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 05/07/2020] [Accepted: 05/16/2020] [Indexed: 06/11/2023]
Abstract
The physicochemical properties of inhalable particles during hazy days have been extensively studied, but their biological health threats have not been well-explored. This study aimed to explore the impacts of haze pollution on airborne bacteria and antibiotic-resistance genes (ARGs) by conducting a comparative study of the bacterial community structure and functions, pathogenic compositions, and ARGs between hazy days and non-hazy days in a cold megacity in Northeast China. The results suggested that bacterial communities were shaped by local weather and customs. In this study, cold-resistant and Chinese sauerkraut-related bacterial compositions were identified as predominant genera. In the comparative analysis, higher proportions of gram-negative bacteria and pathogens were detected on hazy days than on non-hazy days. Pollutants on hazy days provided more nutrients (sulfate, nitrate and ammonium) for bacterial metabolism but also caused more bacterial cell damage and death than on non-hazy days. This study also detected increases in the sub-types and average absolute abundance of airborne resistance genes on hazy days compared to non-hazy days. The results of this study revealed that particle pollution promotes the dissemination and exchange of pathogenic bacteria and ARGs among large urban populations, which leads to a higher potential for human inhalation exposure.
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Affiliation(s)
- Xiazhong Sun
- Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China; School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Dongmei Li
- Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China; School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Bo Li
- Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China; School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Shaojing Sun
- Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China; School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Stephen Dauda Yabo
- Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China; School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jialu Geng
- Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China; School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Lixin Ma
- Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China; School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Hong Qi
- Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China; School of Environment, Harbin Institute of Technology, Harbin 150090, China.
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Allert MJ, Hellinga HW. Harnessing Environmental Ca 2+ for Extracellular Protein Thermostabilization. Biochemistry 2020; 59:3725-3740. [PMID: 32915552 DOI: 10.1021/acs.biochem.0c00449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Ca2+ is the third-most prevalent metal ion in the environment. EF hands are common Ca2+-binding motifs found in both extracellular and intracellular proteins of eukaryotes and prokaryotes. Cytoplasmic EF hand proteins often mediate allosteric control of signal transduction pathway components in response to intracellular Ca2+ concentration fluctuations by coupling Ca2+ binding to changes in protein structure. We show that an extracellular structural Ca2+-binding site mediates protein thermostabilization by such conformational coupling as well. Binding Ca2+ to the EF hand of the extracellular (periplasmic) Escherichia coli glucose-galactose binding protein thermostabilizes this protein by ∼17 K relative to its Ca2+-free form. Using statistical thermodynamic analysis of a fluorescent conjugate of ecGGBP that reports simultaneously on ligand binding and multiple conformational states, we found that its Ca2+-mediated stabilization is determined by conformational coupling mechanisms in two independent conformational exchange reactions. Binding to folded and unfolded states determines the maximum Ca2+-mediated stability. A disorder → order transition accompanies the formation of the Ca2+ complex in the folded state and dictates the minimum Ca2+ concentration at which the Ca2+-bound state becomes dominant. Similar transitions also encode the structural changes necessary for Ca2+-mediated control elements in signal transduction pathways. Ca2+-mediated thermostabilization and allosteric control, therefore, share a fundamental conformational coupling mechanism, which may have implications for the evolution of EF hands.
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Affiliation(s)
- Malin J Allert
- Department of Biochemistry, Duke University Medical Center, P.O. Box 3711, Durham, North Carolina 27710, United States
| | - Homme W Hellinga
- Department of Biochemistry, Duke University Medical Center, P.O. Box 3711, Durham, North Carolina 27710, United States
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25
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Chien CF, Liu CY, Lu YY, Sung YH, Chen KY, Lin NC. HSI-II Gene Cluster of Pseudomonas syringae pv. tomato DC3000 Encodes a Functional Type VI Secretion System Required for Interbacterial Competition. Front Microbiol 2020; 11:1118. [PMID: 32582082 PMCID: PMC7283901 DOI: 10.3389/fmicb.2020.01118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 05/05/2020] [Indexed: 11/13/2022] Open
Abstract
The type VI secretion system (T6SS) is a widespread bacterial nanoweapon used for delivery of toxic proteins into cell targets and contributes to virulence, anti-inflammatory processes, and interbacterial competition. In the model phytopathogenic bacterium Pseudomonas syringae pv. tomato (Pst) DC3000, two T6SS gene clusters, HSI-I and HSI-II, were identified, but their functions remain unclear. We previously reported that hcp2, located in HSI-II, is involved in competition with enterobacteria and yeast. Here, we demonstrated that interbacterial competition of Pst DC3000 against several Gram-negative plant-associated bacteria requires mainly HSI-II activity. By means of a systematic approach using in-frame deletion mutants for each gene in the HSI-II cluster, we identified genes indispensable for Hcp2 expression, Hcp2 secretion and interbacterial competition ability. Deletion of PSPTO_5413 only affected growth in interbacterial competition assays but not Hcp2 secretion, which suggests that PSPTO_5413 might be a putative effector. Moreover, PSPTO_5424, encoding a putative σ54-dependent transcriptional regulator, positively regulated the expression of all three operons in HSI-II. Our discovery that the HSI-II gene cluster gives Pst DC3000 the ability to compete with other plant-associated bacteria could help in understanding a possible mechanism of how phytopathogenic bacteria maintain their ecological niches.
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Affiliation(s)
- Ching-Fang Chien
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - Cheng-Ying Liu
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - Yew-Yee Lu
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - You-Hsing Sung
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - Kuo-Yau Chen
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - Nai-Chun Lin
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
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26
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Stelmakh SA, Grigor’eva MN, Garkusheva NM, Lebedeva SN, Ochirov OS, Mognonov DM, Zhamsaranova SD, Batoev VB. Studies of new biocidal polyguanidines: antibacterial action and toxicity. Polym Bull (Berl) 2020. [DOI: 10.1007/s00289-020-03197-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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27
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Pereira SA, Jesus GFA, Pereira GV, Silva BC, Sá LS, Martins ML, Mouriño JLP. The Chelating Mineral on Organic Acid Salts Modulates the Dynamics and Richness of the Intestinal Microbiota of a Silver Catfish Rhamdia quelen. Curr Microbiol 2020; 77:1483-1495. [PMID: 32236647 DOI: 10.1007/s00284-020-01962-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 03/21/2020] [Indexed: 02/01/2023]
Abstract
The aim of this study was to evaluate the influence of the chelating mineral on propionic acid, calcium or sodium on the composition, dynamics and richness of the intestinal microbiota of a native silver catfish Rhamdia quelen through high-throughput sequencing (HTS). A total of 225 fish (8.43 ± 0.18 g) were distributed in tanks, 15 fish per tank in five groups with three replicates each: Control, Ca-propionate 0.25% (Ca0.25%) Ca-propionate 1% (Ca1%), Na-propionate 0.25% (Na0.25%) and Na-propionate 1% (Na1%). The feed was provided four times a day for 60 days. After experimental period, the fish were fasted for 24 h and the intestine was aseptically collected, pooled by treatment, and fixed in pure absolute ethanol for subsequent DNA extraction and HTS. The HTS showed that the supplementation of the propionic acid chelated to the mineral calcium or sodium in the different concentrations increased the operational taxonomic units and richness in comparison to control group. The main phyla found were Fusobacteria, Firmicutes, Proteobacteria and Bacteroides. Both the fusobacteria and the genus Cetobacterium, especially C. somerae, were positively modulated with Ca0.25% and Na1% supplementation. It can be emphasized that supplementation with calcium or sodium propionate at different concentrations changed the natural microbiota of R. quelen.
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Affiliation(s)
- Scheila A Pereira
- AQUOS - Aquatic Organisms Health Laboratory, Aquaculture Department, Federal University of Santa Catarina (UFSC), Rod. Admar Gonzaga 1346, Florianópolis, SC, 88040-900, Brazil.
| | - Gabriel F A Jesus
- AQUOS - Aquatic Organisms Health Laboratory, Aquaculture Department, Federal University of Santa Catarina (UFSC), Rod. Admar Gonzaga 1346, Florianópolis, SC, 88040-900, Brazil
| | - Gabriella V Pereira
- Fish Nutrition and Health Research Group, School of Biological Sciences, Faculty of Science and Environment, Plymouth University, Plymouth, UK
| | - Bruno C Silva
- EPAGRI - Company of Agricultural Research and Rural Extension of Santa Catarina, Rua Joaquim Garcia, s/n, Camboriú, SC, 88340-000, Brazil
| | - Lúvia S Sá
- AQUOS - Aquatic Organisms Health Laboratory, Aquaculture Department, Federal University of Santa Catarina (UFSC), Rod. Admar Gonzaga 1346, Florianópolis, SC, 88040-900, Brazil
| | - Maurício L Martins
- AQUOS - Aquatic Organisms Health Laboratory, Aquaculture Department, Federal University of Santa Catarina (UFSC), Rod. Admar Gonzaga 1346, Florianópolis, SC, 88040-900, Brazil
| | - José L P Mouriño
- AQUOS - Aquatic Organisms Health Laboratory, Aquaculture Department, Federal University of Santa Catarina (UFSC), Rod. Admar Gonzaga 1346, Florianópolis, SC, 88040-900, Brazil
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FtsA-FtsZ interaction in Vibrio cholerae causes conformational change of FtsA resulting in inhibition of ATP hydrolysis and polymerization. Int J Biol Macromol 2019; 142:18-32. [PMID: 31790740 DOI: 10.1016/j.ijbiomac.2019.11.217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 11/26/2019] [Accepted: 11/26/2019] [Indexed: 11/23/2022]
Abstract
Proper interaction between the divisome proteins FtsA and FtsZ is important for the bacterial cell division which is not well characterized till date. In this study, the objective was to understand the mechanism of FtsA-FtsZ interaction using full-length recombinant proteins. We cloned, over-expressed, purified and subsequently characterized FtsA of Vibrio cholerae (VcFtsA). We found that VcFtsA polymerization assembly was dependent on Ca2+ ions, which is unique among FtsA proteins reported until now. VcFtsA also showed ATPase activity and its assembly was ATP dependent. Binding parameters of the interaction between the two full-length proteins, VcFtsA, and VcFtsZ determined by fluorescence spectrophotometry yielded a Kd value of around 38 μM. The Kd value of the interaction was 3 μM when VcFtsA was in ATP bound state. We found that VcFtsZ after interacting with VcFtsA causes a change of secondary structure in the later one leading to loss of its ability to hydrolyze ATP, subsequently halting the VcFtsA polymerization. On the other hand, a double-mutant of VcFtsA (VcFtsA-D242E,R300E), that does not bind to VcFtsZ, polymerized in the presence of VcFtsZ. Though FtsA proteins among different organisms show 70-80% homology in their sequences, assembly of VcFtsA showed a difference in its regulatory processes.
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29
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Ojennus DD, Bratt NJ, Jones KL, Juers DH. Structural characterization of a prolyl aminodipeptidase (PepX) from Lactobacillus helveticus. Acta Crystallogr F Struct Biol Commun 2019; 75:625-633. [PMID: 31584010 PMCID: PMC6777133 DOI: 10.1107/s2053230x19011774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 08/26/2019] [Indexed: 01/25/2023] Open
Abstract
Prolyl aminodipeptidase (PepX) is an enzyme that hydrolyzes peptide bonds from the N-terminus of substrates when the penultimate amino-acid residue is a proline. Prolyl peptidases are of particular interest owing to their ability to hydrolyze food allergens that contain a high percentage of proline residues. PepX from Lactobacillus helveticus was cloned and expressed in Escherichia coli as an N-terminally His-tagged recombinant construct and was crystallized by hanging-drop vapor diffusion in a phosphate buffer using PEG 3350 as a precipitant. The structure was determined at 2.0 Å resolution by molecular replacement using the structure of PepX from Lactococcus lactis (PDB entry 1lns) as the starting model. Notable differences between the L. helveticus PepX structure and PDB entry 1lns include a cysteine instead of a phenylalanine at the substrate-binding site in the position which confers exopeptidase activity and the presence of a calcium ion coordinated by a calcium-binding motif with the consensus sequence DX(DN)XDG.
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Affiliation(s)
- Deanna Dahlke Ojennus
- Department of Chemistry, Whitworth University, 300 West Hawthorne Road, Spokane, WA 99251, USA
| | - Nicholas J. Bratt
- Department of Chemistry, Whitworth University, 300 West Hawthorne Road, Spokane, WA 99251, USA
| | - Kent L. Jones
- Department of Mathematics and Computer Science, Whitworth University, 300 West Hawthorne Road, Spokane, WA 99251, USA
| | - Douglas H. Juers
- Department of Physics and Program in Biochemistry, Biophysics and Molecular Biology, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99632, USA
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30
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Sharma D, Sharma A, Singh B, Verma SK. Bioinformatic Exploration of Metal-Binding Proteome of Zoonotic Pathogen Orientia tsutsugamushi. Front Genet 2019; 10:797. [PMID: 31608099 PMCID: PMC6769048 DOI: 10.3389/fgene.2019.00797] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/30/2019] [Indexed: 12/21/2022] Open
Abstract
Metal ions are involved in many essential biological processes and are crucial for the survival of all organisms. Identification of metal-binding proteins (MBPs) of human affecting pathogens may provide the blueprint for understanding biological metal usage and their putative roles in pathogenesis. This study is focused on the analysis of MBPs from Orientia tsutsugamushi (Ott), a causal agent of scrub typhus in humans. A total of 321 proteins were predicted as putative MBPs, based on sequence search and three-dimensional structure analysis. Majority of proteins could bind with magnesium, and the order of metal binding was Mg > Ca > Zn > Mn > Fe > Cd > Ni > Co > Cu, respectively. The predicted MBPs were functionally classified into nine broad classes. Among them, gene expression and regulation, metabolism, cell signaling, and transport classes were dominant. It was noted that the putative MBPs were localized in all subcellular compartments of Ott, but majorly found in the cytoplasm. Additionally, it was revealed that out of 321 predicted MBPs 245 proteins were putative bacterial toxins and among them, 98 proteins were nonhomologous to human proteome. Sixty putative MBPs showed the ability to interact with drug or drug-like molecules, which indicate that they may be used as broad-spectrum drug targets. These predicted MBPs from Ott could play vital role(s) in various cellular activities and virulence, hence may serve as plausible therapeutic targets to design metal-based drugs to curtail its infection.
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Affiliation(s)
- Dixit Sharma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, India
| | - Ankita Sharma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, India
| | - Birbal Singh
- ICAR-Indian Veterinary Research Institute, Regional Station, Palampur, India
| | - Shailender Kumar Verma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, India
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31
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Imperato V, Kowalkowski L, Portillo-Estrada M, Gawronski SW, Vangronsveld J, Thijs S. Characterisation of the Carpinus betulus L. Phyllomicrobiome in Urban and Forest Areas. Front Microbiol 2019; 10:1110. [PMID: 31191469 PMCID: PMC6549492 DOI: 10.3389/fmicb.2019.01110] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 05/01/2019] [Indexed: 11/30/2022] Open
Abstract
Urban green areas are highly valued by citizens for their contribution to the quality of life in cities. Plants play an important role in mitigating airborne pollutants and are assisted in this role by the metabolic capacities of the millions of microbial cells that colonize leaf surfaces (phyllosphere). Many factors influence phyllosphere microbial community composition and function, but to what extent does airborne pollution in cities impact the composition of microbial communities and their functional degradation genes? Here we describe the characterization of the phyllospheric bacterial communities of Carpinus betulus L. trees (hornbeam) across three locations: the city center of Warsaw (Poland), a forest in a UNESCO World Heritage Site (Białowieża), and a forest in one of the world’s oldest operational oil fields (Bóbrka). C. betulus contained higher particulate matter (PM) concentrations, with higher concentrations of palladium and radon in the PM, on leaves in Warsaw than in the forests. Volatile organic compound (VOC) analyses of sampled air revealed higher concentrations of butanone methyl propanal, butylbenzene, and cyclohexane in Bóbrka than Warsaw and Białowieża, while in Warsaw, xylene and toluene were higher. Shotgun microbiome sequencing uncovered a dominance of Gammaproteobacteria (71%), mainly Pseudomonas spp., Actinobacteria, Alpha- and Betaproteobacteria, and Firmicutes. Community composition and function differed significantly between the forests and Warsaw city center. Statistically more hydrocarbon degradation genes were found in Białowieża compared to Warsaw and Bóbrka, and in vitro tests of diesel degradation and plant growth promotion traits of culturable representatives revealed that Białowieża held the highest number of bacteria with plant beneficial properties and degradation genes. This study provides the first detailed insights into the microbiome of C. betulus and sets the stage for developing to a more integrated understanding of phyllosphere microbiota in cities, and their relationships with human health.
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Affiliation(s)
- Valeria Imperato
- Department of Biology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Lukasz Kowalkowski
- Department of Biology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium.,Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Warsaw, Poland
| | | | - Stanislaw W Gawronski
- Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Warsaw, Poland
| | - Jaco Vangronsveld
- Department of Biology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium.,Department of Plant Physiology, Faculty of Biology and Biotechnology, Maria Skłodowska-Curie University, Lublin, Poland
| | - Sofie Thijs
- Department of Biology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
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32
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A novel Ca 2+-binding protein influences photosynthetic electron transport in Anabaena sp. PCC 7120. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:519-532. [PMID: 31034800 DOI: 10.1016/j.bbabio.2019.04.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/17/2019] [Accepted: 04/23/2019] [Indexed: 12/25/2022]
Abstract
Ca2+ is a potent signalling molecule that regulates many cellular processes. In cyanobacteria, Ca2+ has been linked to cell growth, stress response and photosynthesis, and to the development of specialist heterocyst cells in certain nitrogen-fixing species. Despite this, the pathways of Ca2+ signal transduction in cyanobacteria are poorly understood, and very few protein components are known. The current study describes a previously unreported Ca2+-binding protein which was called the Ca2+ Sensor EF-hand (CSE), which is conserved in filamentous, nitrogen-fixing cyanobacteria. CSE is shown to bind Ca2+, which induces a conformational change in the protein structure. Poor growth of a strain of Anabaena sp. PCC 7120 overexpressing CSE was attributed to diminished photosynthetic performance. Transcriptomics, biophysics and proteomics analyses revealed modifications in the light-harvesting phycobilisome and photosynthetic reaction centre protein complexes.
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33
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He T, Xie D, Ni J, Li Z. Ca(II) and Mg(II) significantly enhanced the nitrogen removal capacity of Arthrobacter arilaitensis relative to Zn(II) and Ni(II). JOURNAL OF HAZARDOUS MATERIALS 2019; 368:594-601. [PMID: 30716569 DOI: 10.1016/j.jhazmat.2019.01.094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 01/26/2019] [Accepted: 01/28/2019] [Indexed: 06/09/2023]
Abstract
This study investigated the impacts of alkaline-earth metals [Ca(II), Mg(II)] and heavy metals [Zn(II), Ni(II)] on the nitrogen removal capacity of Arthrobacter arilaitensis Y-10. StrainY-10 was able to tolerate 20 mg/L Ca(II) and its ammonium removal efficiency was 100%. 0.5 mg/L Ca(II) effectively promoted total nitrogen removal from wastewater containing nitrite. Mg(II) supplementation substantially enhanced the bacterial growth and nitrogen reduction. As Mg(II) concentrations increased from 0 to 2 mg/L, the ammonium, nitrate and nitrite removal efficiencies increased by 40.62%, 69.91% and 64.68%, respectively. Although the nitrogen removal ability of strain Y-10 was sharply hindered by Zn(II) and Ni(II), it occurred continuously even when the Zn(II) concentration reached 30 mg/L. However, the ammonium and total nitrogen removal almost stopped at 8 mg/L Ni(II), and the denitrification capacity was lost when the Ni(II) concentration exceeded 1 mg/L. The results demonstrate that Ca(II) and especially Mg(II) could significantly enhance the nitrogen removal capacity of Arthrobacter arilaitensis relative to Zn(II) and Ni(II).
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Affiliation(s)
- Tengxia He
- Chongqing Key Laboratory of Soil Multiscale Interfacial Process, College of Resources and Environment, Southwest University, Chongqing, 400716, China
| | - Deti Xie
- Chongqing Key Laboratory of Soil Multiscale Interfacial Process, College of Resources and Environment, Southwest University, Chongqing, 400716, China
| | - Jiupai Ni
- Chongqing Key Laboratory of Soil Multiscale Interfacial Process, College of Resources and Environment, Southwest University, Chongqing, 400716, China
| | - Zhenlun Li
- Chongqing Key Laboratory of Soil Multiscale Interfacial Process, College of Resources and Environment, Southwest University, Chongqing, 400716, China.
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34
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Meena LS. Interrelation of Ca2+ and PE_PGRS proteins during Mycobacterium tuberculosis pathogenesis. J Biosci 2019. [DOI: 10.1007/s12038-018-9828-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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35
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Green RT, East AK, Karunakaran R, Downie JA, Poole PS. Transcriptomic analysis of Rhizobium leguminosarum bacteroids in determinate and indeterminate nodules. Microb Genom 2019; 5:e000254. [PMID: 30777812 PMCID: PMC6421345 DOI: 10.1099/mgen.0.000254] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/15/2019] [Indexed: 01/25/2023] Open
Abstract
Two common classes of nitrogen-fixing legume root nodules are those that have determinate or indeterminate meristems, as in Phaseolus bean and pea, respectively. In indeterminate nodules, rhizobia terminally differentiate into bacteroids with endoreduplicated genomes, whereas bacteroids from determinate nodules are less differentiated and can regrow. We used RNA sequencing to compare bacteroid gene expression in determinate and indeterminate nodules using two Rhizobium leguminosarum strains whose genomes differ due to replacement of the symbiosis (Sym) plasmid pRP2 (strain Rlp4292) with pRL1 (strain RlvA34), thereby switching symbiosis hosts from Phaseolus bean (determinate nodules) to pea (indeterminate nodules). Both bacteroid types have gene expression patterns typical of a stringent response, a stressful environment and catabolism of dicarboxylates, formate, amino acids and quaternary amines. Gene expression patterns were indicative that bean bacteroids were more limited for phosphate, sulphate and iron than pea bacteroids. Bean bacteroids had higher levels of expression of genes whose products are predicted to be associated with metabolite detoxification or export. Pea bacteroids had increased expression of genes associated with DNA replication, membrane synthesis and the TCA (tricarboxylic acid) cycle. Analysis of bacteroid-specific transporter genes was indicative of distinct differences in sugars and other compounds in the two nodule environments. Cell division genes were down-regulated in pea but not bean bacteroids, while DNA synthesis was increased in pea bacteroids. This is consistent with endoreduplication of pea bacteroids and their failure to regrow once nodules senesce.
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Affiliation(s)
- R. T. Green
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - A. K. East
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - R. Karunakaran
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - J. A. Downie
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - P. S. Poole
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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36
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Xie Z, Fan C, Lu R, Liu P, Wang B, Du S, Jin C, Deng S, Li Y. Characteristics of ambient bioaerosols during haze episodes in China: A review. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 243:1930-1942. [PMID: 30237031 DOI: 10.1016/j.envpol.2018.09.051] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 08/21/2018] [Accepted: 09/07/2018] [Indexed: 05/22/2023]
Abstract
Frequent low visibility, haze pollution caused by heavy fine particulate matter (PM2.5) loading, has been entailing significant environmental issues and health risks in China since 2013. A substantial fraction of bioaerosols was observed in PM (1.5-15%) during haze periods with intensive pollution. However, systematic and consistent results of the variations of bioaerosol characteristics during haze pollution are lacking. The role of bioaerosols in air quality and interaction with environment conditions are not yet well characterized. The present article provides an overview of the state of bioaerosol research during haze episodes based on numerous recent studies over the past decade, focusing on concentration, size distribution, community structure, and influence factors. Examples of insightful results highlighted the characteristics of bioaerosols at different air pollution levels and their pollution effects. We summarize the influences of meteorological and environmental factors on the distribution of bioaerosols. Further studies on bioaerosols, applying standardized sampling and identification criteria and investigating the influence of mechanisms of environmental or pollution factors on bioaerosols as well as the sources of bioaerosols are proposed.
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Affiliation(s)
- Zhengsheng Xie
- School of Environmental Science and Engineering, Chang'an University, Xi'an 710054, China
| | - Chunlan Fan
- School of Environmental Science and Engineering, Chang'an University, Xi'an 710054, China
| | - Rui Lu
- School of Environmental Science and Engineering, Chang'an University, Xi'an 710054, China
| | - Pengxia Liu
- School of Environmental Science and Engineering, Chang'an University, Xi'an 710054, China
| | - Beibei Wang
- School of Environmental Science and Engineering, Chang'an University, Xi'an 710054, China
| | - Shengli Du
- School of Environmental Science and Engineering, Chang'an University, Xi'an 710054, China
| | - Cheng Jin
- School of Architecture, Chang'an University, Xi'an, 710061, China
| | - Shunxi Deng
- School of Environmental Science and Engineering, Chang'an University, Xi'an 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Xi'an, 710054, China
| | - Yanpeng Li
- School of Environmental Science and Engineering, Chang'an University, Xi'an 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Xi'an, 710054, China; Shaanxi Key Laboratory of Land Consolidation, Xi'an 710054, China.
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Sun Y, Xu S, Zheng D, Li J, Tian H, Wang Y. Effects of haze pollution on microbial community changes and correlation with chemical components in atmospheric particulate matter. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 637-638:507-516. [PMID: 29754085 DOI: 10.1016/j.scitotenv.2018.04.203] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 03/31/2018] [Accepted: 04/15/2018] [Indexed: 05/14/2023]
Abstract
In this study, particulate matter (PM) with aerodynamic diameters of ≤2.5 and ≤10 μm (PM2.5 and PM10, respectively), which was found at different concentrations in spring, was collected in Beijing. The chemical composition and bacterial community diversity of PM were determined, and the relationship between them was studied by 16S rRNA sequencing and mathematical statistics. Chemical composition analysis revealed greater relative percentages of total organic compounds (TOC) and secondary ions (NO3-, SO42-, and NH4+). The concentrations of Ca2+, Na+, Mg2+, K+ and SO42- increased in high-concentration PM, which was associated with the contribution of soil, dust and soot. Microbiological analysis revealed 1191 operational taxonomic units. Microbial community structure was stable at the phylum level. The most abundant phyla were Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes and Cyanobacteria. Community clustering analysis at the genus level showed that the difference in bacterial community structure between different PM concentrations (clean air vs. smog) was greater than that between different particle sizes. The dominant genera varied in different concentrations of PM. An unclassified genus of Cyanobacteria and Comamonadaceae were most abundant in low- and high-concentration PM, respectively. The microbial community structure was dynamic at the genus level due to different environmental factors. The dominant bacteria in high-concentration PM were widely distributed in soils, indicating that the soil contributed more to the increase in the PM. The individual microbes that were detected did not increase significantly as the PM concentration increased. The bacterial community structure was strongly correlated with K+, Ca2+, Na+, Mg2+, SO42- and TOC in high-concentration PM and had a good correlation with NO3-, Cl-, NH4+ and TIC in low-concentration PM. Soil and dust contributed to the increase in the concentration of the particles, and the relevant chemical components also produced differences in the bacterial community structure in different concentrations of PM.
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Affiliation(s)
- Yujiao Sun
- College of Water Sciences, Beijing Normal University, Beijing 100875, China.
| | - Shangwei Xu
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Danyang Zheng
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Jie Li
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Hezhong Tian
- School of Environment, Beijing Normal University, Beijing 100875, China.
| | - Yong Wang
- School of Environment, Beijing Normal University, Beijing 100875, China
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Zhang X, Manukumar H, Rakesh K, Karthik C, Nagendra Prasad H, Swamy SN, Mallu P, Eissa Mohammed YH, Qin HL. Role of BP*C@AgNPs in Bap-dependent multicellular behavior of clinically important methicillin-resistant Staphylococcus aureus (MRSA) biofilm adherence: A key virulence study. Microb Pathog 2018; 123:275-284. [DOI: 10.1016/j.micpath.2018.07.025] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 12/19/2022]
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Tal N, Rudnick-Glick S, Grinberg I, Natan M, Banin E, Margel S. Engineering of a New Bisphosphonate Monomer and Nanoparticles of Narrow Size Distribution for Antibacterial Applications. ACS OMEGA 2018; 3:1458-1469. [PMID: 30023805 PMCID: PMC6044825 DOI: 10.1021/acsomega.7b01686] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/15/2018] [Indexed: 06/08/2023]
Abstract
In recent years, many bacteria have developed resistance to commonly used antibiotics. It is well-known that calcium is essential for bacterial function and cell wall stability. Bisphosphonates (BPs) have high affinity to calcium ions and are effective calcium chelators. Therefore, BPs could potentially be used as antibacterial agents. This article provides a detailed description regarding the synthesis of a unique BP vinylic monomer MA-Glu-BP (methacrylate glutamate bisphosphonate) and polyMA-Glu-BP nanoparticles (NPs) for antibacterial applications. polyMA-Glu-BP NPs were synthesized by dispersion copolymerization of the MA-Glu-BP monomer with the primary amino monomer N-(3-aminopropyl)methacrylamide hydrochloride (APMA) and the cross-linker monomer tetra ethylene glycol diacrylate, to form cross-linked NPs with a narrow size distribution. The size and size distribution of polyMA-Glu-BP NPs were controlled by changing various polymerization parameters. Near-infrared fluorescent polyMA-Glu-BP NPs were prepared by covalent binding of the dye cyanine7 N-hydroxysuccinimide to the primary amino groups belonging to the APMA monomeric units on the polyMA-Glu-BP NPs. The affinity of the near-infrared fluorescent polyMA-Glu-BP NPs toward calcium was demonstrated in vitro by a coral model. Cytotoxicity, cell uptake, and antibacterial properties of the polyMA-Glu-BP NPs against two common bacterial pathogens representing Gram-negative bacteria, Escherichia coli and Pseudomonas aeruginosa, and two representing Gram-positive bacteria, Listeria innocua and Staphylococcus aureus, were then demonstrated.
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Affiliation(s)
- Nimrod Tal
- The Institute of Nanotechnology
and Advanced Materials, Department
of Chemistry, and The Mina and Everard Goodman Faculty of Life Sciences, The Institute
for Advanced Materials and Nanotechnology, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Safra Rudnick-Glick
- The Institute of Nanotechnology
and Advanced Materials, Department
of Chemistry, and The Mina and Everard Goodman Faculty of Life Sciences, The Institute
for Advanced Materials and Nanotechnology, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Igor Grinberg
- The Institute of Nanotechnology
and Advanced Materials, Department
of Chemistry, and The Mina and Everard Goodman Faculty of Life Sciences, The Institute
for Advanced Materials and Nanotechnology, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Michal Natan
- The Institute of Nanotechnology
and Advanced Materials, Department
of Chemistry, and The Mina and Everard Goodman Faculty of Life Sciences, The Institute
for Advanced Materials and Nanotechnology, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Ehud Banin
- The Institute of Nanotechnology
and Advanced Materials, Department
of Chemistry, and The Mina and Everard Goodman Faculty of Life Sciences, The Institute
for Advanced Materials and Nanotechnology, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Shlomo Margel
- The Institute of Nanotechnology
and Advanced Materials, Department
of Chemistry, and The Mina and Everard Goodman Faculty of Life Sciences, The Institute
for Advanced Materials and Nanotechnology, Bar-Ilan University, Ramat-Gan 52900, Israel
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40
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Urdaneta V, Casadesús J. Interactions between Bacteria and Bile Salts in the Gastrointestinal and Hepatobiliary Tracts. Front Med (Lausanne) 2017; 4:163. [PMID: 29043249 PMCID: PMC5632352 DOI: 10.3389/fmed.2017.00163] [Citation(s) in RCA: 231] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 09/19/2017] [Indexed: 12/25/2022] Open
Abstract
Bile salts and bacteria have intricate relationships. The composition of the intestinal pool of bile salts is shaped by bacterial metabolism. In turn, bile salts play a role in intestinal homeostasis by controlling the size and the composition of the intestinal microbiota. As a consequence, alteration of the microbiome-bile salt homeostasis can play a role in hepatic and gastrointestinal pathological conditions. Intestinal bacteria use bile salts as environmental signals and in certain cases as nutrients and electron acceptors. However, bile salts are antibacterial compounds that disrupt bacterial membranes, denature proteins, chelate iron and calcium, cause oxidative damage to DNA, and control the expression of eukaryotic genes involved in host defense and immunity. Bacterial species adapted to the mammalian gut are able to endure the antibacterial activities of bile salts by multiple physiological adjustments that include remodeling of the cell envelope and activation of efflux systems and stress responses. Resistance to bile salts permits that certain bile-resistant pathogens can colonize the hepatobiliary tract, and an outstanding example is the chronic infection of the gall bladder by Salmonella enterica. A better understanding of the interactions between bacteria and bile salts may inspire novel therapeutic strategies for gastrointestinal and hepatobiliary diseases that involve microbiome alteration, as well as novel schemes against bacterial infections.
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Affiliation(s)
- Verónica Urdaneta
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Josep Casadesús
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
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Herrmann J, Jabbarpour F, Bargar PG, Nomellini JF, Li PN, Lane TJ, Weiss TM, Smit J, Shapiro L, Wakatsuki S. Environmental Calcium Controls Alternate Physical States of the Caulobacter Surface Layer. Biophys J 2017; 112:1841-1851. [PMID: 28494955 PMCID: PMC5425405 DOI: 10.1016/j.bpj.2017.04.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/28/2017] [Accepted: 04/06/2017] [Indexed: 11/23/2022] Open
Abstract
Surface layers (S-layers) are paracrystalline, proteinaceous structures found in most archaea and many bacteria. Often the outermost cell envelope component, S-layers serve diverse functions including aiding pathogenicity and protecting against predators. We report that the S-layer of Caulobacter crescentus exhibits calcium-mediated structural plasticity, switching irreversibly between an amorphous aggregate state and the crystalline state. This finding invalidates the common assumption that S-layers serve only as static wall-like structures. In vitro, the Caulobacter S-layer protein, RsaA, enters the aggregate state at physiological temperatures and low divalent calcium ion concentrations. At higher concentrations, calcium ions stabilize monomeric RsaA, which can then transition to the two-dimensional crystalline state. Caulobacter requires micromolar concentrations of calcium for normal growth and development. Without an S-layer, Caulobacter is even more sensitive to changes in environmental calcium concentration. Therefore, this structurally dynamic S-layer responds to environmental conditions as an ion sensor and protects Caulobacter from calcium deficiency stress, a unique mechanism of bacterial adaptation. These findings provide a biochemical and physiological basis for RsaA's calcium-binding behavior, which extends far beyond calcium's commonly accepted role in aiding S-layer biogenesis or oligomerization and demonstrates a connection to cellular fitness.
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Affiliation(s)
- Jonathan Herrmann
- Department of Structural Biology, Stanford University, Stanford, California; Bioscience Division, SLAC National Accelerator Laboratory, Menlo Park, California.
| | - Fatemeh Jabbarpour
- Department of Structural Biology, Stanford University, Stanford, California
| | | | - John F Nomellini
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Po-Nan Li
- Department of Electrical Engineering, Stanford University, Stanford, California
| | - Thomas J Lane
- Bioscience Division, SLAC National Accelerator Laboratory, Menlo Park, California
| | - Thomas M Weiss
- Bioscience Division, SLAC National Accelerator Laboratory, Menlo Park, California
| | - John Smit
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lucy Shapiro
- Department of Developmental Biology, Stanford University, Stanford, California.
| | - Soichi Wakatsuki
- Department of Structural Biology, Stanford University, Stanford, California; Bioscience Division, SLAC National Accelerator Laboratory, Menlo Park, California.
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42
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Xu C, Wei M, Chen J, Wang X, Zhu C, Li J, Zheng L, Sui G, Li W, Wang W, Zhang Q, Mellouki A. Bacterial characterization in ambient submicron particles during severe haze episodes at Ji'nan, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 580:188-196. [PMID: 28017418 DOI: 10.1016/j.scitotenv.2016.11.145] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 11/12/2016] [Accepted: 11/21/2016] [Indexed: 05/14/2023]
Abstract
In January 2014, severe haze episodes which sweep across Chinese cities have attracted public concern and interest at home and abroad. In addition to the physicochemical properties of air pollutants, bacteria are thought to be responsible for the spread of respiratory diseases and various allergies. We attempted the bacterial characterization of submicron particles (PM0.18-0.32, PM0.32-0.56, and PM0.56-1) under severe haze episodes using high-throughput sequencing and real-time quantitative PCR detecting system based on 21 samples collected from January to March 2014 at Ji'nan, China. The high bacterial concentration in PM0.32-0.56 (7314cells m-3), PM0.18-0.32 (7212cells m-3), and PM0.56-1 (6982cells m-3) showed significant negative correlations with SO2, NO2, and O3. Under sufficient sequencing depth, 37 phyla, 71 classes, 137 orders, 236 families, and 378 genera were classified, and the bacterial community structure varied significantly in different size fractions. For example, Holophagaceae (Acidobacteria) in PM0.32-0.56 showed 6-fold higher abundance than that in PM0.18-0.32. Moreover, functional categories and bacterial species (Lactococcus piscium, Pseudomonas fragi, Streptococcus agalactiae, and Pseudomonas cichorii) that may potentially be responsible for infections and allergies were also discovered. Source track analysis showed that the ambient bacteria mainly originated from soils, leaf surfaces, and feces. Our results highlighted the importance of airborne microbial communities by understanding the concentration, structure, ecological and health effects, especially those in submicron particles during haze episodes.
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Affiliation(s)
- Caihong Xu
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China
| | - Min Wei
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China
| | - Jianmin Chen
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China; Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP), Fudan Tyndall Centre, Department of Environmental Science & Engineering, Fudan University, Shanghai 200433, China.
| | - Xinfeng Wang
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China
| | - Chao Zhu
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China
| | - Jiarong Li
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China
| | - Lulu Zheng
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP), Fudan Tyndall Centre, Department of Environmental Science & Engineering, Fudan University, Shanghai 200433, China
| | - Guodong Sui
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP), Fudan Tyndall Centre, Department of Environmental Science & Engineering, Fudan University, Shanghai 200433, China
| | - Weijun Li
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China
| | - Wenxing Wang
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China
| | - Qingzhu Zhang
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China
| | - Abdelwahid Mellouki
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China; Institut de Combustion, Aérothermique, Réactivité et Environnement, CNRS, 45071 Orléans cedex 02, France
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43
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Marchadier E, Oates ME, Fang H, Donoghue PCJ, Hetherington AM, Gough J. Evolution of the Calcium-Based Intracellular Signaling System. Genome Biol Evol 2016; 8:2118-32. [PMID: 27358427 PMCID: PMC4987107 DOI: 10.1093/gbe/evw139] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
To progress our understanding of molecular evolution from a collection of well-studied genes toward the level of the cell, we must consider whole systems. Here, we reveal the evolution of an important intracellular signaling system. The calcium-signaling toolkit is made up of different multidomain proteins that have undergone duplication, recombination, sequence divergence, and selection. The picture of evolution, considering the repertoire of proteins in the toolkit of both extant organisms and ancestors, is radically different from that of other systems. In eukaryotes, the repertoire increased in both abundance and diversity at a far greater rate than general genomic expansion. We describe how calcium-based intracellular signaling evolution differs not only in rate but in nature, and how this correlates with the disparity of plants and animals.
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Affiliation(s)
- Elodie Marchadier
- Life Sciences Building, University of Bristol, United Kingdom GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Matt E Oates
- Department of Computer Sciences, University of Bristol, United Kingdom
| | - Hai Fang
- Department of Computer Sciences, University of Bristol, United Kingdom
| | | | | | - Julian Gough
- Department of Computer Sciences, University of Bristol, United Kingdom
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Walter J, Lynch F, Battchikova N, Aro EM, Gollan PJ. Calcium impacts carbon and nitrogen balance in the filamentous cyanobacterium Anabaena sp. PCC 7120. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3997-4008. [PMID: 27012282 PMCID: PMC4915528 DOI: 10.1093/jxb/erw112] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Calcium is integral to the perception, communication and adjustment of cellular responses to environmental changes. However, the role of Ca(2+) in fine-tuning cellular responses of wild-type cyanobacteria under favourable growth conditions has not been examined. In this study, extracellular Ca(2+) has been altered, and changes in the whole transcriptome of Anabaena sp. PCC 7120 have been evaluated under conditions replete of carbon and combined nitrogen. Ca(2+) induced differential expression of many genes driving primary cellular metabolism, with transcriptional regulation of carbon- and nitrogen-related processes responding with opposing trends. However, physiological effects of these transcriptional responses on biomass accumulation, biomass composition, and photosynthetic activity over the 24h period following Ca(2+) adjustment were found to be minor. It is well known that intracellular carbon:nitrogen balance is integral to optimal cell growth and that Ca(2+) plays an important role in the response of heterocystous cyanobacteria to combined-nitrogen deprivation. This work adds to the current knowledge by demonstrating a signalling role of Ca(2+) for making sensitive transcriptional adjustments required for optimal growth under non-limiting conditions.
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Affiliation(s)
- Julia Walter
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014 Turku, Finland
| | - Fiona Lynch
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014 Turku, Finland
| | - Natalia Battchikova
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014 Turku, Finland
| | - Eva-Mari Aro
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014 Turku, Finland
| | - Peter J Gollan
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014 Turku, Finland
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45
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Zhang ZZ, Cheng YF, Zhou YH, Buayi X, Jin RC. Roles of EDTA washing and Ca²⁺ regulation on the restoration of anammox granules inhibited by copper(II). JOURNAL OF HAZARDOUS MATERIALS 2016; 301:92-99. [PMID: 26342580 DOI: 10.1016/j.jhazmat.2015.08.036] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 08/11/2015] [Accepted: 08/22/2015] [Indexed: 06/05/2023]
Abstract
We investigated the feasibility of using ethylene diamine tetraacetic acid (EDTA) washing followed by Ca(2+) enhancement for the recovery of anammox reactors inhibited by Cu(II). Kinetic experiments and batch activity assays were employed to determine the optimal concentration of EDTA and washing time; and the performance and physiological dynamics were tracked by continuous-flow monitoring to evaluate the long-term effects. The two-step desorption process revealed that the Cu in anammox granules was primarily introduced via adsorption (approximately, 80.5%), and the portion of Cu in the dispersible layer was predominant (accounting for 71.1%). Afterwards, the Cu internalized in the cells (approximately, 14.7%) could diffuse out of the cells and be gradually washed out of the reactor over the next 20 days. The Ca(2+) addition that followed led to an accelerated nitrogen removal rate recovery slope (0.1491 kgN m(-3) d(-2)) and a normal biomass growth rate (0.054 d(-1)). The nitrogen removal rate returned to normal levels within 90 days and gradual improvements in granular characteristics were also achieved. Therefore, this study provides a new insight that externally removing the adsorbed heavy metals followed by internally repairing the metabolic system may represent an optimal restoration strategy for anammox consortium damaged by heavy metals.
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Affiliation(s)
- Zheng-Zhe Zhang
- Department of Environmental Science and Engineering, Hangzhou Normal University, Hangzhou 310036, China; Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, Hangzhou Normal University, Hangzhou 310036, China
| | - Ya-Fei Cheng
- Department of Environmental Science and Engineering, Hangzhou Normal University, Hangzhou 310036, China; Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, Hangzhou Normal University, Hangzhou 310036, China
| | - Yu-Huang Zhou
- Department of Environmental Science and Engineering, Hangzhou Normal University, Hangzhou 310036, China; Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, Hangzhou Normal University, Hangzhou 310036, China
| | - Xiemuguli Buayi
- Department of Environmental Science and Engineering, Hangzhou Normal University, Hangzhou 310036, China; Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, Hangzhou Normal University, Hangzhou 310036, China
| | - Ren-Cun Jin
- Department of Environmental Science and Engineering, Hangzhou Normal University, Hangzhou 310036, China; Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, Hangzhou Normal University, Hangzhou 310036, China.
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Changes in Sodium, Calcium, and Magnesium Ion Concentrations That Inhibit Geobacillus Biofilms Have No Effect on Anoxybacillus flavithermus Biofilms. Appl Environ Microbiol 2015; 81:5115-22. [PMID: 26002898 DOI: 10.1128/aem.01037-15] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 05/13/2015] [Indexed: 11/20/2022] Open
Abstract
This study investigated the effects of varied sodium, calcium, and magnesium concentrations in specialty milk formulations on biofilm formation by Geobacillus spp. and Anoxybacillus flavithermus. The numbers of attached viable cells (log CFU per square centimeter) after 6 to 18 h of biofilm formation by three dairy-derived strains of Geobacillus and three dairy-derived strains of A. flavithermus were compared in two commercial milk formulations. Milk formulation B had relatively high sodium and low calcium and magnesium concentrations compared with those of milk formulation A, but the two formulations had comparable fat, protein, and lactose concentrations. Biofilm formation by the three Geobacillus isolates was up to 4 log CFU cm(-2) lower in milk formulation B than in milk formulation A after 6 to 18 h, and the difference was often significant (P ≤ 0.05). However, no significant differences (P ≤ 0.05) were found when biofilm formations by the three A. flavithermus isolates were compared in milk formulations A and B. Supplementation of milk formulation A with 100 mM NaCl significantly decreased (P ≤ 0.05) Geobacillus biofilm formation after 6 to 10 h. Furthermore, supplementation of milk formulation B with 2 mM CaCl2 or 2 mM MgCl2 significantly increased (P ≤ 0.05) Geobacillus biofilm formation after 10 to 18 h. It was concluded that relatively high free Na(+) and low free Ca(2+) and Mg(2+) concentrations in milk formulations are collectively required to inhibit biofilm formation by Geobacillus spp., whereas biofilm formation by A. flavithermus is not impacted by typical cation concentration differences of milk formulations.
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Moscatiello R, Zaccarin M, Ercolin F, Damiani E, Squartini A, Roveri A, Navazio L. Identification of ferredoxin II as a major calcium binding protein in the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. BMC Microbiol 2015; 15:16. [PMID: 25648224 PMCID: PMC4322793 DOI: 10.1186/s12866-015-0352-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 01/16/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Legumes establish with rhizobial bacteria a nitrogen-fixing symbiosis which is of the utmost importance for both plant nutrition and a sustainable agriculture. Calcium is known to act as a key intracellular messenger in the perception of symbiotic signals by both the host plant and the microbial partner. Regulation of intracellular free Ca(2+) concentration, which is a fundamental prerequisite for any Ca(2+)-based signalling system, is accomplished by complex mechanisms including Ca(2+) binding proteins acting as Ca(2+) buffers. In this work we investigated the occurrence of Ca(2+) binding proteins in Mesorhizobium loti, the specific symbiotic partner of the model legume Lotus japonicus. RESULTS A soluble, low molecular weight protein was found to share several biochemical features with the eukaryotic Ca(2+)-binding proteins calsequestrin and calreticulin, such as Stains-all blue staining on SDS-PAGE, an acidic isoelectric point and a Ca(2+)-dependent shift of electrophoretic mobility. The protein was purified to homogeneity by an ammonium sulfate precipitation procedure followed by anion-exchange chromatography on DEAE-Cellulose and electroendosmotic preparative electrophoresis. The Ca(2+) binding ability of the M. loti protein was demonstrated by (45)Ca(2+)-overlay assays. ESI-Q-TOF MS/MS analyses of the peptides generated after digestion with either trypsin or endoproteinase AspN identified the rhizobial protein as ferredoxin II and confirmed the presence of Ca(2+) adducts. CONCLUSIONS The present data indicate that ferredoxin II is a major Ca(2+) binding protein in M. loti that may participate in Ca(2+) homeostasis and suggest an evolutionarily ancient origin for protein-based Ca(2+) regulatory systems.
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Affiliation(s)
- Roberto Moscatiello
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35131, Padova, Italy.
| | - Mattia Zaccarin
- Department of Molecular Medicine, University of Padova, Viale G. Colombo 3, 35131, Padova, Italy.
| | - Flavia Ercolin
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35131, Padova, Italy.
| | - Ernesto Damiani
- Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35131, Padova, Italy.
| | - Andrea Squartini
- Department of Agronomy, Food, Natural Resources, Animals and Environment, DAFNAE, University of Padova, Viale dell'Università 16, 35020, Legnaro, Padova, Italy.
| | - Antonella Roveri
- Department of Molecular Medicine, University of Padova, Viale G. Colombo 3, 35131, Padova, Italy.
| | - Lorella Navazio
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35131, Padova, Italy.
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Calcium binding proteins and calcium signaling in prokaryotes. Cell Calcium 2014; 57:151-65. [PMID: 25555683 DOI: 10.1016/j.ceca.2014.12.006] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/08/2014] [Accepted: 12/09/2014] [Indexed: 11/20/2022]
Abstract
With the continued increase of genomic information and computational analyses during the recent years, the number of newly discovered calcium binding proteins (CaBPs) in prokaryotic organisms has increased dramatically. These proteins contain sequences that closely resemble a variety of eukaryotic calcium (Ca(2+)) binding motifs including the canonical and pseudo EF-hand motifs, Ca(2+)-binding β-roll, Greek key motif and a novel putative Ca(2+)-binding domain, called the Big domain. Prokaryotic CaBPs have been implicated in diverse cellular activities such as division, development, motility, homeostasis, stress response, secretion, transport, signaling and host-pathogen interactions. However, the majority of these proteins are hypothetical, and only few of them have been studied functionally. The finding of many diverse CaBPs in prokaryotic genomes opens an exciting area of research to explore and define the role of Ca(2+) in organisms other than eukaryotes. This review presents the most recent developments in the field of CaBPs and novel advancements in the role of Ca(2+) in prokaryotes.
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Norris V, Reusch RN, Igarashi K, Root-Bernstein R. Molecular complementarity between simple, universal molecules and ions limited phenotype space in the precursors of cells. Biol Direct 2014; 10:28. [PMID: 25470982 PMCID: PMC4264330 DOI: 10.1186/s13062-014-0028-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 11/24/2014] [Indexed: 01/29/2023] Open
Abstract
Background Fundamental problems faced by the protocells and their modern descendants include how to go from one phenotypic state to another; escape from a basin of attraction in the space of phenotypes; reconcile conflicting growth and survival strategies (and thereby live on ‘the scales of equilibria’); and create a coherent, reproducible phenotype from a multitude of constituents. Presentation of the hypothesis The solutions to these problems are likely to be found with the organic and inorganic molecules and inorganic ions that constituted protocells, which we term SUMIs for Simple Universal Molecules and Ions. These SUMIs probably included polyphosphate (PolyP) as a source of energy and of phosphate; poly-(R)-3-hydroxybutyrate (PHB) as a source of carbon and as a transporter in association with PolyP; polyamines as a source of nitrogen; lipids as precursors of membranes; as well as peptides, nucleic acids, and calcium. Here, we explore the hypothesis that the direct interactions between PHB, PolyP, polyamines and lipids – modulated by calcium – played a central role in solving the fundamental problems faced by early and modern cells. Testing the hypothesis We review evidence that SUMIs (1) were abundant and available to protocells; (2) are widespread in modern cells; (3) interact with one another and other cellular constituents to create structures with new functions surprisingly similar to those of proteins and RNA; (4) are essential to creating coherent phenotypes in modern bacteria. SUMIs are therefore natural candidates for reducing the immensity of phenotype space and making the transition from a “primordial soup” to living cells. Implications of the hypothesis We discuss the relevance of the SUMIs and their interactions to the ideas of molecular complementarity, composomes (molecular aggregates with hereditary properties based on molecular complementarity), and a prebiotic ecology of co-evolving populations of composomes. In particular, we propose that SUMIs might limit the initial phenotype space of composomes in a coherent way. As examples, we propose that acidocalcisomes arose from interactions and self-selection among SUMIs and that the phosphorylation of proteins in modern cells had its origin in the covalent modification of proteins by PHB. Reviewers This article was reviewed by Doron Lancet and Kepa Ruiz-Mirazo.
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