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Guo Y, Li X, Fan D, Xue J, Han J, Zhu Y. Lysobacter may drive the hormetic effects of Pb on soil alkaline phosphatase. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:17779-17788. [PMID: 32162228 DOI: 10.1007/s11356-020-08278-2] [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: 11/10/2019] [Accepted: 02/28/2020] [Indexed: 06/10/2023]
Abstract
It has become increasingly recognized that hormesis phenomena exist in soil ecosystem, but the research on the hormetic responses of soil enzymes are still limited. This study was conducted to investigate the hormetic effects of lead (Pb) on the activity of soil alkaline phosphatase (ALP) and the associated microbial groups. Soils were treated by adding Pb (NO3)2 solution with 0, 10, 100, 500, 1000, 2000, 4000, and 5000 mg/kg of Pb, respectively. A moist heat sterilization method (121 °C × 30 min) was used to discriminate the microbial effect on soil ALP hormesis from other factors. The bacterial community composition and abundance in the control (CK) and Pb-treated soils were detected by the high-throughput sequencing technique. The ALP activity at doses of 500-1000 mg/kg of Pb was significantly higher than that of CK (0 mg/kg of Pb), showing a typical inverted U-shaped dose response with the stimulation magnitude of 9.8-10.3% within 48 h of incubation. In addition, ALP activity decreased by 80% on average after soil sterilization. Analysis of bacterial community composition indicated that the relative abundance of Lysobacter at 1000 mg Pb/kg was higher than that of CK at genus level, with the increase of 69.82%. The highly significant correlation between soil ALP activities and relative abundance of Lysobacter indicated that this bacterial genus could possibly contribute to the hormetic responses of soil ALP to added doses of Pb in soils.
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Affiliation(s)
- Yanhui Guo
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
- National Positioning Observation Station of Hongze Lake Wetland Ecosystem in Jiangsu Province, Hongze, 223100, Jiangsu, China
| | - Xiuzhi Li
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Diwu Fan
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Jianming Xue
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
- Scion, Private Bag, 29237, Christchurch, New Zealand
| | - Jiangang Han
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Yongli Zhu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.
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Zimmerman AE, Martiny AC, Allison SD. Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes. THE ISME JOURNAL 2013; 7:1187-99. [PMID: 23303371 PMCID: PMC3660669 DOI: 10.1038/ismej.2012.176] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 11/20/2012] [Accepted: 12/01/2012] [Indexed: 11/08/2022]
Abstract
Understanding the relationship between prokaryotic traits and phylogeny is important for predicting and modeling ecological processes. Microbial extracellular enzymes have a pivotal role in nutrient cycling and the decomposition of organic matter, yet little is known about the phylogenetic distribution of genes encoding these enzymes. In this study, we analyzed 3058 annotated prokaryotic genomes to determine which taxa have the genetic potential to produce alkaline phosphatase, chitinase and β-N-acetyl-glucosaminidase enzymes. We then evaluated the relationship between the genetic potential for enzyme production and 16S rRNA phylogeny using the consenTRAIT algorithm, which calculated the phylogenetic depth and corresponding 16S rRNA sequence identity of clades of potential enzyme producers. Nearly half (49.2%) of the genomes analyzed were found to be capable of extracellular enzyme production, and these were non-randomly distributed across most prokaryotic phyla. On average, clades of potential enzyme-producing organisms had a maximum phylogenetic depth of 0.008004-0.009780, though individual clades varied broadly in both size and depth. These values correspond to a minimum 16S rRNA sequence identity of 98.04-98.40%. The distribution pattern we found is an indication of microdiversity, the occurrence of ecologically or physiologically distinct populations within phylogenetically related groups. Additionally, we found positive correlations among the genes encoding different extracellular enzymes. Our results suggest that the capacity to produce extracellular enzymes varies at relatively fine-scale phylogenetic resolution. This variation is consistent with other traits that require a small number of genes and provides insight into the relationship between taxonomy and traits that may be useful for predicting ecological function.
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Affiliation(s)
- Amy E Zimmerman
- Department of Ecology and Evolutionary Biology, University of California Irvine, CA 92697, USA.
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Yeung SL, Cheng C, Lui TKO, Tsang JSH, Chan WT, Lim BL. Purple acid phosphatase-like sequences in prokaryotic genomes and the characterization of an atypical purple alkaline phosphatase from Burkholderia cenocepacia J2315. Gene 2009; 440:1-8. [PMID: 19376213 DOI: 10.1016/j.gene.2009.04.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Revised: 03/31/2009] [Accepted: 04/07/2009] [Indexed: 10/20/2022]
Abstract
Purple acid phosphatases (PAP) are a group of dimetallic phosphohydrolase first identified in eukaryotes. Bioinformatics analysis revealed 57 prokaryotic PAP-like sequences in the genomes of 43 bacteria and 4 cyanobacteria species. A putative PAP gene (BcPAP) from the bacteria Burkholderia cenocepacia J2315 was chosen for further studies. Synteny analysis showed that this gene is present as an independent gene in most of the members of the genus Burkholderia. The predicted 561 a.a. polypeptide of BcPAP was found to harbour all the conserved motifs of the eukaryotic PAPs and an N-terminal twin-arginine translocation signal. Expression and biochemical characterization of BcPAP in Escherichia coli revealed that this enzyme has a relatively narrow substrate spectrum, preferably towards phosphotyrosine, phosphoserine and phosphoenolpyruvate. Interestingly, this enzyme was found to have a pH optimum at 8.5, rather than an acidic optima exhibited by eukaryotic PAPs. BcPAP contains a dimetallic ion centre composed of Fe and Zn, and site-directed mutagenesis confirmed that BcPAP utilizes the invariant residues for metal-ligation and catalysis. The enzyme is secreted by the wild type bacteria and its expression is regulated by the availability of orthophosphate. Our findings suggest that not all members in the PAP family have acidic pH optimum and broad substrate specificity.
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Affiliation(s)
- Sin-Lui Yeung
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
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Kriakov J, Lee SH, Jacobs WR. Identification of a regulated alkaline phosphatase, a cell surface-associated lipoprotein, in Mycobacterium smegmatis. J Bacteriol 2003; 185:4983-91. [PMID: 12897018 PMCID: PMC166462 DOI: 10.1128/jb.185.16.4983-4991.2003] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although alkaline phosphatases are common in a wide variety of bacteria, there has been no prior evidence for alkaline phosphatases in Mycobacterium smegmatis. Here we report that transposon insertions in the pst operon, encoding homologues of an inorganic phosphate transporter, leads to constitutive expression of a protein with alkaline phosphatase activity. DNA sequence analysis revealed that M. smegmatis does indeed have a phoA gene that shows high homology to other phoA genes. The M. smegmatis phoA gene was shown to be induced by phosphate starvation and thus negatively regulated by the pst operon. Interestingly, the putative M. smegmatis PhoA has a hydrophobic N-terminal domain which resembles a lipoprotein signal sequence. The M. smegmatis PhoA was demonstrated to be an exported protein associated with the cell surface. Furthermore, immunoprecipitation of PhoA from [(14)C]acetate-labeled M. smegmatis cell lysates demonstrated that this phosphatase is a lipoprotein.
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Affiliation(s)
- Jordan Kriakov
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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Martinez-Canamero M, Ortiz-Codorniu C, Extremera AL, Munoz-Dorado J, Arias JM. mlpB, a gene encoding a new lipoprotein in Myxococcus xanthus. J Appl Microbiol 2002; 92:134-9. [PMID: 11849337 DOI: 10.1046/j.1365-2672.2002.01517.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS To search for and study the genes involved in the regulation of phosphate in the soil developmental bacterium Myxococcus xanthus. METHODS AND RESULTS The mlpB gene encoding a 149 residue polypeptide was identified while screening for genes with products related to phosphate metabolism. The amino terminal 19 residues of MlpB encode a typical prokaryotic signal sequence with a putative lipoprotein cleavage site. CONCLUSIONS In this study, a new myxobacterial putative lipoprotein is reported. The data suggest that MlpB may be involved in the secretion of phosphate-related proteins. SIGNIFICANCE AND IMPACT OF THE STUDY Soil bacteria have complex regulatory systems for using inorganic phosphate. This nutrient is limiting in the environment, and has a critical importance for growth and in the initiation of differentiation for developmental bacteria. A number of proteins are involved in all these processes, including membrane lipoproteins, which are being increasingly studied in M. xanthus.
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Affiliation(s)
- M Martinez-Canamero
- Departamento de Microbiologia, Facultad de Ciencias, Universidad de Granada, Spain.
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Moura RS, Martı N JF, Martı N A, Liras P. Substrate analysis and molecular cloning of the extracellular alkaline phosphatase of Streptomyces griseus. MICROBIOLOGY (READING, ENGLAND) 2001; 147:1525-1533. [PMID: 11390683 DOI: 10.1099/00221287-147-6-1525] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Streptomyces species secrete large amounts of alkaline phosphatase (AP) enzymes that have not been characterized so far. An AP has been purified to homogeneity from cultures of Streptomyces griseus IMRU 3570. The enzyme has a monomer size of 62 kDa and is processed in the culture to a 33 kDa protein as shown by immunoblotting. The enzyme was purified by ammonium sulfate precipitation, CM-Sephadex cationic exchange, chromatofocusing and HPLC Sphaerogel 3000SW filtration. The pure enzyme uses a variety of organic phosphorylated compounds as substrates. The N-terminal end of the mature protein was found to be RLREDPFTLGVASGDPHP. The gene phoA has been cloned using as probe an oligomer based on the N-terminal sequence of the S. griseus AP. phoA encodes a protein of 62678 Da with low homology to the AP of Escherichia coli. The phoA gene was found to be homologous to three alkaline-phosphatase-encoding genes previously identified in the Streptomyces coelicolor genome. On the basis of the optimal pH, substrate specificity and differences in amino acid sequence of motifs defining the active centre of APs, the S. griseus AP uses a wide range of organic phosphate substrates and is different from the phosphatases of Gram-negative bacteria.
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Affiliation(s)
- Rute S Moura
- Instituto de Biotecnologı́a de León INBIOTEC, Parque Cientı́fico de León, Avda del Real no. 1, 24006 León, Spain1
| | - Juan F Martı N
- Area de Microbioloı́a, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain2
- Instituto de Biotecnologı́a de León INBIOTEC, Parque Cientı́fico de León, Avda del Real no. 1, 24006 León, Spain1
| | - Alicia Martı N
- Area de Microbioloı́a, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain2
| | - Paloma Liras
- Area de Microbioloı́a, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain2
- Instituto de Biotecnologı́a de León INBIOTEC, Parque Cientı́fico de León, Avda del Real no. 1, 24006 León, Spain1
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Hirani TA, Suzuki I, Murata N, Hayashi H, Eaton-Rye JJ. Characterization of a two-component signal transduction system involved in the induction of alkaline phosphatase under phosphate-limiting conditions in Synechocystis sp. PCC 6803. PLANT MOLECULAR BIOLOGY 2001; 45:133-144. [PMID: 11289505 DOI: 10.1023/a:1006425214168] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The gene products of sll0337 and slr0081 in Synechocystis sp. PCC 6803 have been identified as the homologues of the Escherichia coli phosphate-sensing histidine kinase PhoR and response regulator PhoB, respectively. Interruption of sll0337, the gene encoding the histidine protein kinase, by a spectinomycin-resistance cassette blocked the induction of alkaline phosphatase activity under phosphate-limiting conditions. A similar result was obtained when slr0081, the gene encoding the response regulator, was interrupted with a cassette conferring resistance to kanamycin. In addition, the phosphate-specific transport system was not up-regulated in our mutants when phosphate was limiting. Unlike other genes for bacterial phosphate-sensing two-component systems, sll0337 and slr0081 are not present in the same operon. Although there are three assignments for putative alkaline phosphatase genes in the Synechocystis sp. PCC 6803 genome, only sll0654 expression was detected by northern analysis under phosphate limitation. This gene codes for a 149 kDa protein that is homologous to the cyanobacterial alkaline phosphatase reported in Synechococcus sp. PCC 7942 [Ray, J.M., Bhaya, D., Block, M.A. and Grossman, A.R. (1991) J. Bact. 173: 4297-4309]. An alignment identified a conserved 177 amino acid domain that was found at the N-terminus of the protein encoded by sll0654 but at the C-terminus of the protein in Synechococcus sp. PCC 7942.
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Affiliation(s)
- T A Hirani
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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Feller G, D'Amico S, Benotmane AM, Joly F, Van Beeumen J, Gerday C. Characterization of the C-terminal propeptide involved in bacterial wall spanning of alpha-amylase from the psychrophile Alteromonas haloplanctis. J Biol Chem 1998; 273:12109-15. [PMID: 9575155 DOI: 10.1074/jbc.273.20.12109] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The antarctic psychrophile Alteromonas haloplanctis secretes a Ca2+- and Cl--dependent alpha-amylase. The nucleotide sequence of the amy gene and the amino acid sequences of the gene products indicate that the alpha-amylase precursor is a preproenzyme composed by the signal peptide (24 residues), the mature alpha-amylase (453 residues, 49 kDa), and a long C-terminal propeptide or secretion helper (192 residues, 21 kDa). In cultures of the wild-type strain, the 70-kDa precursor is secreted at the mid-exponential phase and is cleaved by a nonspecific protease into the mature enzyme and the propeptide. The purified C-terminal propeptide displays several features common to beta-pleated transmembrane proteins. It has no intramolecular chaperone function because active alpha-amylase is expressed by Escherichia coli in the absence of the propeptide coding region. In E. coli, the 70-kDa precursor is directed toward the supernatant. When the alpha-amylase coding region is excised from the gene, the secretion helper can still promote its own membrane spanning. It can also accept a foreign passenger, as shown by the extracellular routing of a beta-lactamase-propeptide fusion protein.
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Affiliation(s)
- G Feller
- Laboratory of Biochemistry, Institute of Chemistry B6, University of Liege, B-4000 Liege, Belgium.
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Lin D, McBride MJ. Development of techniques for the genetic manipulation of the gliding bacteria Lysobacter enzymogenes and Lysobacter brunescens. Can J Microbiol 1996; 42:896-902. [PMID: 8864212 DOI: 10.1139/m96-115] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Lysobacter enzymogenes and Lysobacter brunescens are Gram-negative gliding bacteria that belong to the gamma subgroup of the proteobacteria. As a first step toward a molecular analysis of Lysobacter gliding motility, we developed techniques to genetically manipulate these bacteria. Cosmid pSUP106 of the broad host range incompatibility group Q (Inc Q) was introduced into L. enzymogenes and L. brunescens by conjugation and electroporation. pSUP106 replicated stably in both organisms and conferred antibiotic resistance. We also identified several other plasmids (pKT210, pH1JI) that functioned in L. enzymogenes and a transposon (mini-Tn5Sp) that functioned in L. brunescens. The identification of these tools allows genetic analysis of Lysobacter gliding motility, exoenzyme production, and production of antibiotics and other secondary metabolites.
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Affiliation(s)
- D Lin
- Department of Biological Sciences, University of Wisconsin-Milwaukee, 53201, USA
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Abstract
We have analysed the response of the acidophilic chemolithotroph Thiobacillus ferrooxidans to phosphate starvation. Cultivation of the bacteria in the absence of added phosphate induced a remarkable filamentation of the cells. Polyacrylamide gel electrophoresis revealed several proteins whose levels increased upon phosphate limitation, as well as some polypeptides that were exclusively synthesized under this growth limitation. One of the proteins whose level increased by the lack of phosphate was apparently an acid phosphatase with a pH optimum of about 3.8, and a molecular mass of 26 kDa, which was located in the periplasm. The N-terminal sequence of a 26 kDa protein derepressed by starvation, which may correspond to the T. ferrooxidans starvation, which may correspond to the T. ferrooxidans phosphatase, showed 30% and 35% identity with the known sequence of Lysobacter enzymogenes and Escherichia coli alkaline phosphatases, respectively.
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Affiliation(s)
- M Seeger
- Departamento de Bioquímica, Facultad de Medicina, Universidad de Chile, Santiago
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Abstract
The unifying feature of all proteins that are transported out of the cytoplasm of gram-negative bacteria by the general secretory pathway (GSP) is the presence of a long stretch of predominantly hydrophobic amino acids, the signal sequence. The interaction between signal sequence-bearing proteins and the cytoplasmic membrane may be a spontaneous event driven by the electrochemical energy potential across the cytoplasmic membrane, leading to membrane integration. The translocation of large, hydrophilic polypeptide segments to the periplasmic side of this membrane almost always requires at least six different proteins encoded by the sec genes and is dependent on both ATP hydrolysis and the electrochemical energy potential. Signal peptidases process precursors with a single, amino-terminal signal sequence, allowing them to be released into the periplasm, where they may remain or whence they may be inserted into the outer membrane. Selected proteins may also be transported across this membrane for assembly into cell surface appendages or for release into the extracellular medium. Many bacteria secrete a variety of structurally different proteins by a common pathway, referred to here as the main terminal branch of the GSP. This recently discovered branch pathway comprises at least 14 gene products. Other, simpler terminal branches of the GSP are also used by gram-negative bacteria to secrete a more limited range of extracellular proteins.
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Affiliation(s)
- A P Pugsley
- Unité de Génétique Moléculaire, Institut Pasteur, Paris, France
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