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Jung H, Inaba Y, Banta S. Genetic engineering of the acidophilic chemolithoautotroph Acidithiobacillus ferrooxidans. Trends Biotechnol 2021; 40:677-692. [PMID: 34794837 DOI: 10.1016/j.tibtech.2021.10.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/21/2022]
Abstract
There are several natural and anthropomorphic environments where iron- and/or sulfur-oxidizing bacteria thrive in extremely acidic conditions. These acidophilic chemolithautotrophs play important roles in biogeochemical iron and sulfur cycles, are critical catalysts for industrial metal bioleaching operations, and have underexplored potential in future biotechnological applications. However, their unique growth conditions complicate the development of genetic techniques. Over the past few decades genetic tools have been successfully developed for Acidithiobacillus ferrooxidans, which serves as a model organism that exhibits both iron- and sulfur-oxidizing capabilities. Conjugal transfer of plasmids has enabled gene overexpression, gene knockouts, and some preliminary metabolic engineering. We highlight the development of genetic systems and recent genetic engineering of A. ferrooxidans, and discuss future perspectives.
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Affiliation(s)
- Heejung Jung
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, USA
| | - Yuta Inaba
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, USA
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, USA.
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Singh SK, Banerjee PC. High-yielding plasmid extraction method from acidophilic heterotrophic bacteria of the genus Acidiphilium. Anal Biochem 2006; 356:229-34. [PMID: 16859629 DOI: 10.1016/j.ab.2006.06.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2006] [Revised: 06/08/2006] [Accepted: 06/11/2006] [Indexed: 11/18/2022]
Abstract
Plasmid yield from Acidiphilium strains always had been poor following various standard methods. We adopted some simple modifications in the alkaline lysis procedure to get a better yield of plasmid from these bacteria. An approximately 10- to 20-fold increase in the plasmid yield was achieved when harvested Acidiphilium cells were preincubated 16-20 h at pH 6 in nitrogen-free medium. Another independent approach showed that freezing (-18 to -20 degrees C) of the harvested cells initially and at two subsequent steps in the alkaline lysis procedure of plasmid DNA extraction improved the yield further by 1.5- to 3-fold. The combination of these changes yielded at least 15- to 30-fold more plasmid from various Acidiphilium strains as compared with standard methods.
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Ghosh S, Mahapatra NR, Nandi S, Banerjee PC. Integration of Metal-Resistant Determinants from the Plasmid of an Acidocella Strain into the Chromosome of Escherichia coli DH5?*. Curr Microbiol 2005; 50:28-32. [PMID: 15702259 DOI: 10.1007/s00284-004-4370-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2004] [Accepted: 07/10/2004] [Indexed: 10/25/2022]
Abstract
Acidophilic bacteria of mine origin are ideal systems for studying microbial metal resistance because of their ability to grow in the presence of high concentrations of metal salts. We have previously shown that the metal-resistant transformants obtained after transformation of Escherichia coli DH5alpha with plasmid DNA preparation from Acidocella sp. strain GS19h did not contain any plasmid suggesting chromosomal integration of the plasmid(s) (Appl Environ Microbiol 1997; 63: 4523-4527). The present study provides evidence in support of this suggestion. The pulsed field gel electrophoresis (PFGE) pattern of genomic DNA of the plasmidless metal-resistant transformants differed markedly from that of the untransformed DH5alpha strain. Moreover, when the recombinant plasmids constructed by cloning plasmid DNA fragments of the Acidocella strain GS19h in the vector pBluescript II KS+ were used to transform E. coli DH5alpha strain, no plasmid DNA was detected in some of the zinc- and ampicillin-resistant (ZnrAmpr) clones. The PFGE pattern of genomic DNA of such a transformed clone also differed markedly from that of the parent strain, suggesting chromosomal integration of the recombinant plasmid(s) containing both ampicillin- and zinc-resistance determinants. This observation was further supported by hybridization of chromosomal DNA of the plasmidless ZnrAmpr E. coli DH5alpha clone with the probes made from the plasmid DNA of strain GS19h and the vector DNA. Thus, this study corroborates our previous finding and documents the phenomenon of integration of metal-resistant determinants from the Acidocella GS19h plasmid(s) into the chromosome of E. coli DH5alpha.
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Affiliation(s)
- Sajalendu Ghosh
- Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata, 700032, India
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Karavaiko GI, Turova TP, Kondrat'eva TF, Lysenko AM, Kolganova TV, Ageeva SN, Muntyan LN, Pivovarova TA. Phylogenetic heterogeneity of the species Acidithiobacillus ferrooxidans. Int J Syst Evol Microbiol 2003; 53:113-119. [PMID: 12656161 DOI: 10.1099/ijs.0.02319-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Polyphasic genotypic analysis of 25 Acidithiobacillus ferrooxidans strains isolated from ores and ore concentrates collected in different regions of the world showed considerable strain heterogeneity. Restriction patterns of the chromosomal DNA of these strains obtained by PFGE were specific for each strain. According to the degree of DNA relatedness, 17 of the 23 strains studied were divided into four genomovars. Six independent, considerably divergent strains could not be assigned to any of the genomovars. A comparison of nearly complete nucleotide sequences of the 16S rDNA of five representatives of the genomovars (including the type strain of A. ferrooxidans, ATCC 23270T) with those of species of the genus Acidithiobacillus available from GenBank showed that most of the A. ferrooxidans strains, together with the type strain and some other strains of the species Acidithiobacillus thiooxidans, comprised a monophyletic cluster. Within this major cluster, A. ferrooxidans strains fell into four phylogenetic groups that were equidistant from the phylogenetic group of A. thiooxidans strains. In general, the distribution of strains among the phylogenetic groups correlated with their distribution among the genomovars, except that the representatives of two different genomovars fell into one phylogenetic group. Thus, at least two levels of phylogenetic heterogeneity for A. ferrooxidans have been found. The phylogenetic heterogeneity of A. ferrooxidans strains, which are phenotypically indistinguishable, suggests the occurrence of microevolutionary processes in different econiches. This should be taken into account in the biohydrometallurgical applications of A. ferrooxidans strains.
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Affiliation(s)
- Grigorii I Karavaiko
- Institute of Microbiology, Russian Academy of Sciences, pr. 60-letiya Oktyabrya 7, k. 2, Moscow 117811, Russia
| | - Tat'yana P Turova
- Institute of Microbiology, Russian Academy of Sciences, pr. 60-letiya Oktyabrya 7, k. 2, Moscow 117811, Russia
| | - Tamara F Kondrat'eva
- Institute of Microbiology, Russian Academy of Sciences, pr. 60-letiya Oktyabrya 7, k. 2, Moscow 117811, Russia
| | - Anatoli M Lysenko
- Institute of Microbiology, Russian Academy of Sciences, pr. 60-letiya Oktyabrya 7, k. 2, Moscow 117811, Russia
| | - Tat'yana V Kolganova
- Centre for Bioengineering, Russian Academy of Sciences, pr. 60-letiya Oktyabrya 7, k. 1, Moscow 117312, Russia
| | - Svetlana N Ageeva
- Institute of Microbiology, Russian Academy of Sciences, pr. 60-letiya Oktyabrya 7, k. 2, Moscow 117811, Russia
| | - Lyudmila N Muntyan
- Institute of Microbiology, Russian Academy of Sciences, pr. 60-letiya Oktyabrya 7, k. 2, Moscow 117811, Russia
| | - Tat'yana A Pivovarova
- Institute of Microbiology, Russian Academy of Sciences, pr. 60-letiya Oktyabrya 7, k. 2, Moscow 117811, Russia
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Abstract
The whole nucleotide sequence of pT3.2I, the smallest plasmid of the acidophilic bacterium Thiobacillus T3.2, has been determined. pT3.2I is 15,390 bp long with a 53.7% GC content. Different regions can be defined in it: one 2569-bp putative insertion sequence similar to other insertion sequences of some Agrobacterium Ti plasmids; and a longer sequence, which occurs in two almost identical copies, differing only in a 1-bp deletion (6406 and 6405 bp). Several open reading frames and some smaller sequences were found in this duplicated region: ORFA and ORFG, encoding a putative polyol dehydrogenase and a putative RepA replication protein, respectively, an 83-bp sequence which could code for an antisense RNA, and a 36-bp region highly homologous to ori sequences of ColE2- and ColE3-related plasmids. Another putative gene, ORFH, is only present in the longer copy of this region (it is deleted in the short copy) and might encode a 90-amino-acid polypeptide which could act as a second replication protein, RepB. Based on sequence comparisons, pT3. 2I can be related to plasmids in the pColE2-CA42 incB incompatibility group.
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Affiliation(s)
- T Aparicio
- Department of Biochemistry and Molecular Biology, Complutense University of Madrid, Madrid, 28040, Spain
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Ghosh S, Mahapatra NR, Banerjee PC. Metal resistance in Acidocella strains and plasmid-mediated transfer of this characteristic to Acidiphilium multivorum and Escherichia coli. Appl Environ Microbiol 1997; 63:4523-7. [PMID: 9361438 PMCID: PMC168771 DOI: 10.1128/aem.63.11.4523-4527.1997] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Acidophilic heterotrophic strain GS19h of the genus Acidocella exhibited extremely high resistance to CdSO4 and ZnSO4, with a MIC of 1 M for each. The respective MICs for an Acidocella aminolytica strain were 400 and 600 mM. The MICs of NiSO4 for the above strains were 200 and 175 mM, respectively. These strains were also resistant to CuSO4, the MICs being 20 and 40 mM, respectively. An Acidocella facilis strain showed resistance only to ZnSO4, with a MIC of 150 mM. The metal salts, in general, extended the lag period, log period, and generation time, with decreases in growth rate and optimum growth. A. aminolytica and strain GS19h each contain more than one plasmid, while A. facilis contains none. After transformation by electroporation with the plasmid preparation from strain GS19h, an Acidiphilium multivorum strain became highly resistant to cadmium and zinc, and the plasmid profile of the transformed cells was found to differ from that of the original Acidiphilium multivorum strain. Escherichia coli HB101 and DH5 alpha also exhibited more resistance to these metals, especially zinc, after transformation with the total plasmid preparation of strain GS19h or a 24.0-MDa plasmid of the same strain, although no plasmid was detected in the transformed cells. Thus, the results derived mainly through genetic experiments demonstrate for the first time the plasmid-mediated transfer of metal resistance for an acidophilic bacterium.
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Affiliation(s)
- S Ghosh
- Indian Institute of Chemical Biology, Calcutta, India
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Petkova S, Groudeva V. Iron and Sulfur Oxidation by Thiobacillus Ferrooxidansand Tolerance to Copper and Zinc Ions. BIOTECHNOL BIOTEC EQ 1997. [DOI: 10.1080/13102818.1997.10818925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Peng JB, Yan WM, Bao XZ. Expression of Heterogenous Arsenic Resistance Genes in the Obligately Autotrophic Biomining Bacterium
Thiobacillus ferrooxidans. Appl Environ Microbiol 1994; 60:2653-6. [PMID: 16349341 PMCID: PMC201699 DOI: 10.1128/aem.60.7.2653-2656.1994] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two arsenic-resistant plasmids were constructed and introduced into
Thiobacillus ferrooxidans
strains by conjugation. The plasmids with the replicon of wide-host-range plasmid RSF1010 were stable in
T. ferrooxidans.
The arsenic resistance genes originating from the heterotroph were expressed in this obligately autotrophic bacterium, but the promoter derived from
T. ferrooxidans
showed no special function in its original host.
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Affiliation(s)
- J B Peng
- Institute of Microbiology, Shandong University, Jinan 250100, People's Republic of China
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Kusano T, Sugawara K, Inoue C, Takeshima T, Numata M, Shiratori T. Electrotransformation of Thiobacillus ferrooxidans with plasmids containing a mer determinant. J Bacteriol 1992; 174:6617-23. [PMID: 1400213 PMCID: PMC207636 DOI: 10.1128/jb.174.20.6617-6623.1992] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The mer operon from a strain of Thiobacillus ferrooxidans (C. Inoue, K. Sugawara, and T. Kusano, Mol. Microbiol. 5:2707-2718, 1991) consists of the regulatory gene merR and an operator-promoter region followed by merC and merA structural genes and differs from other known gram-negative mer operons. We have constructed four potential shuttle plasmids composed of a T. ferrooxidans-borne cryptic plasmid, a pUC18 plasmid, and the above-mentioned mer determinant as a selectable marker. Mercury ion-sensitive T. ferrooxidans strains were electroporated with constructed plasmids, and one strain, Y4-3 (of 30 independent strains tested), was found to have a transformation efficiency of 120 to 200 mercury-resistant colonies per microgram of plasmid DNA. This recipient strain was confirmed to be T. ferrooxidans by physiological, morphological, and chemotaxonomical data. The transformants carried a plasmid with no physical rearrangements through 25 passages under no selective pressure. Cell extracts showed mercury ion-dependent NADPH oxidation activity.
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Affiliation(s)
- T Kusano
- Laboratory of Plant Genetic Engineering, Akita Prefectural College of Agriculture, Japan
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