Two Copies of form I RuBisCO genes in Acidithiobacillus ferrooxidans ATCC 23270

Acidithiobacillus ferrooxidans ATCC 23270 possesses two copies of form I ribulose bisphosphate carboxylase/oxygenase (RuBisCO). The nucleotide sequence identity between the two large and two small subunit peptides was 75% and 58%, respectively. It is proposed that the two copies resulted from lateral gene transfer. Received: 27 October 2000 / Accepted 7 December 2001     

A stoichiometric model of Acidithiobacillus ferrooxidans ATCC 23270 for metabolic flux analysis

A stoichiometric model of Acidithiobacillus ferrooxidans based on the sequenced genome from strain ATCC 23270 is derived and parameterized using genome/pathway databases. The model describes the main aspects of catabolism and anabolism. By the construction and utilization of the mathematical determination of the network, metabolic flux analysis is performed for such a bacterium for the first time and results are successfully verified by comparison to literature values. This first metabolic model of A. ferrooxidans is able to simulate the main aspects of metabolism and will be useful for further investigation and improvement of bioleaching procedures. Biotechnol. Bioeng. 2009;102: 1448–1459. © 2008 Wiley Periodicals, Inc.     

Increase in Fe2+-producing activity during growth of Acidithiobacillus ferrooxidans ATCC23270 on sulfur

When Acidithiobacillus ferrooxidans ATCC23270 cells, grown for many generations on sulfur were grown in sulfur medium with and without Fe(3+), the bacterium markedly increased not only in iron oxidase activity but also in Fe(2+)-producing sulfide:ferric ion oxidoreductase (SFORase) activity during the early log phase, and retained part of these activities during the late log phase. The activity of SFORase, which catalyzes the production of Fe(2+) from Fe(3+) and sulfur, of sulfur-grown cells was approximately 10-20 fold higher than that of iron-grown cells. aa(3) type cytochrome c oxidase, an important component of iron oxidase in A. ferrooxidans, was partially purified from sulfur-grown cells. A. ferrooxidans ATCC23270 cells grown for many generations on sulfur had the ability to grow on iron as rapidly as that did iron-grown cells. These results suggest that both iron oxidase and Fe(2+)-producing SFORase have a role in the energy generation of A. ferrooxidans ATCC23270 from sulfur.     

Cloning, expression and bioinformatics analysis of ATP sulfurylase from Acidithiobacillus ferrooxidans ATCC 23270 in Escherichia coli

Molecular studies of enzymes involved in sulfite oxidation in Acidithiobacillus ferrooxidans have not yet been developed, especiallyin the ATP sulfurylase (ATPS) of these acidophilus tiobacilli that have importance in biomining. This enzyme synthesizes ATP andsulfate from adenosine phosphosulfate (APS) and pyrophosphate (PPi), final stage of the sulfite oxidation by these organisms inorder to obtain energy. The atpS gene (1674 bp) encoding the ATPS from Acidithiobacillus ferrooxidans ATCC 23270 was amplifiedusing PCR, cloned in the pET101-TOPO plasmid, sequenced and expressed in Escherichia coli obtaining a 63.5 kDa ATPSrecombinant protein according to SDS-PAGE analysis. The bioinformatics and phylogenetic analyses determined that the ATPSfrom A. ferrooxidans presents ATP sulfurylase (ATS) and APS kinase (ASK) domains similar to ATPS of Aquifex aeolicus, probably ofa more ancestral origin. Enzyme activity towards ATP formation was determined by quantification of ATP formed from E. coli cellextracts, using a bioluminescence assay based on light emission by the luciferase enzyme. Our results demonstrate that therecombinant ATP sulfurylase from A. ferrooxidans presents an enzymatic activity for the formation of ATP and sulfate, and possiblyis a bifunctional enzyme due to its high homology to the ASK domain from A. aeolicus and true kinases.     

Expression and function of two chaperone proteins,AtGroEL and AtGroES,from Acidithiobacillus ferrooxidans ATCC 23270

Two molecular chaperone genes encoding the Acidithiobacillus ferrooxidans Hsp60 (AtGroEL) and Hsp10 (AtGroES), respectively were introduced into Escherichia coli using the pLM1 expression vector. Then the AtGroEL and AtGroES proteins were overexpressed successfully in Escherichia coli BL21 (DE3), and purified by one-step immobilized metal affinity chromatography. The ATPase assay showed that the proteins were in active form, and the ATPase activity of AtGroEL was temperature dependent with an optimal temperature of 50°C, but the co-chaperonin AtGroES inhibited the ATPase activity of AtGroEL. The chaperonin function of the recombinant proteins was examined using three different protein substrates in vitro, and the results showed that AtGroEL/AtGroES chaperone system could facilitate the refolding of the thermodenatured rusticyanin and recover the activity of thermodenatured ArsH protein. In addition, it could improve the thermal stability of xylanase. Molecular modelling for AtGroEL protein revealed that residues of Tyr199, Ser201, Tyr203, Phe204, Leu234, Leu237, Leu259, Val263 and Val264 were necessary for binding the denatured polypeptides.     

Identification of putative sulfurtransferase genes in the extremophilic Acidithiobacillus ferrooxidans ATCC 23270 genome: structural and functional characterization of the proteins

Eight nucleotide sequences containing a single rhodanese domain were found in the Acidithiobacillus ferrooxidans ATCC 23270 genome: p11, p14, p14.3, p15, p16, p16.2, p21, and p28. Amino acids sequence comparisons allowed us to identify the potentially catalytic Cys residues and other highly conserved rhodanese family features in all eight proteins. The genomic contexts of some of the rhodanese-like genes and the determination of their expression at the mRNA level by using macroarrays suggested their implication in sulfur oxidation and metabolism, formation of Fe-S clusters or detoxification mechanisms. Several of the putative rhodanese genes were successfully isolated, cloned and overexpressed in E. coli and their thiosulfate:cyanide sulfurtransferase (TST) and 3-mercaptopyruvate/cyanide sulfurtransferase (MST) activities were determined. Based on their sulfurtransferase activities and on structural comparisons of catalytic sites and electrostatic potentials between homology- modeled A. ferrooxidans rhodaneses and the reported crystal structures of E. coli GlpE (TST) and SseA (MST) proteins, two of the rhodanese-like proteins (P15 and P16.2) could clearly be defined as TSTs, and P14 and P16 could possibly correspond to MSTs. Nevertheless, several of the eight A. ferrooxidans rhodanese-like proteins may have some different functional activities yet to be discovered.     

Ferrous iron oxidation by foam immobilized Acidithiobacillus ferrooxidans: Experiments and modeling

Ferrous iron bio‐oxidation by Acidithiobacillus ferrooxidans immobilized on polyurethane foam was investigated. Cells were immobilized on foams by placing them in a growth environment and fully bacterially activated polyurethane foams (BAPUFs) were prepared by serial subculturing in batches with partially bacterially activated foam (pBAPUFs). The dependence of foam density on cell immobilization process, the effect of pH and BAPUF loading on ferrous oxidation were studied to choose operating parameters for continuous operations. With an objective to have high cell densities both in foam and the liquid phase, pretreated foams of density 50 kg/m³ as cell support and ferrous oxidation at pH 1.5 to moderate the ferric precipitation were preferred. A novel basket‐type bioreactor for continuous ferrous iron oxidation, which features a multiple effect of stirred tank in combination with recirculation, was designed and operated. The results were compared with that of a free cell and a sheet‐type foam immobilized reactors. A fivefold increase in ferric iron productivity at 33.02 g/h/L of free volume in foam was achieved using basket‐type bioreactor when compared to a free cell continuous system. A mathematical model for ferrous iron oxidation by Acidithiobacillus ferrooxidans cells immobilized on polyurethane foam was developed with cell growth in foam accounted by an effectiveness factor. The basic parameters of simulation were estimated using the experimental data on free cell growth as well as from cell attachment to foam under nongrowing conditions. The model predicted the phase of both oxidation of ferrous in shake flasks by pBAPUFs as well as by fully activated BAPUFs for different cell loadings in foam. Model for stirred tank basket bioreactor predicted within 5% both transient and steady state of the experiments closely for the simulated dilution rates. Bio‐oxidation at high Fe²⁺ concentrations were simulated with experiments when substrate and product inhibition coefficients were factored into cell growth kinetics. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

固定化Acidithiobacillus ferrooxidans对Fe2+氧化及其生物反应器研究进展

Acidithiobacillus ferrooxidans 对Fe2+的生物氧化是一个非常重要的反应过程, 在生物浸矿、H2S等废气的脱硫、含重金属污泥和酸性矿坑废水的处理等领域有着重要的应用。近些年来,大量的研究主要集中A. ferrooxidans及其反应过程等方面,然而,A. ferrooxidans对Fe2+的催化氧化速率缓慢和稳定性欠佳等问题仍然限制了其商业应用。因此,对A. ferrooxidans的固定化及其生物反应器研究是该技术进一步发展的关键。本文评述了A. ferrooxidans最新应用、存在的问题和解决办法,重点比较了目前文献中报道的各种A. ferrooxidans固定材料、方法,并对目前采用的各种固定化A. ferrooxidans生物反应系统的效率和结构等方面进行了讨论和分析。     

Xylanase formation by Sclerotium rolfsii: effect of growth substrates and development of a culture medium using statistically designed experiments

A culture medium for increased xylanase formation by a wild strain of Sclerotium rolfsii was optimized by applying statistically designed experiments. The optimization process was divided into three basic steps. In the initial phase of screening, two different fractional factorial plans, a Graeco-Latin square design and a folded Plackett-Burman design, were employed. From the list of medium components the relevant variables for xylanase formation (cellulose, peptone, and trace elements) were identified. The second step of optimization used a central composite experimental design to calculate a predictive model. In this phase only the two most important factors, i. e. cellulose and peptone from meat, were considered. The third step of verification validated the results of the optimization. Optimal concentrations of cellulose and peptone were found to be 42.6 and 80.0 g 1^–1, respectively. Shaken flask cultivations of S. rolfsii using the optimized medium yielded a maximum xylanase activity of 394 IU ml^–1 (6,570 nkat ml^–1) within 13 days. Growth on the optimized medium also resulted in elevated levels of other hemicellulolytic enzyme activities including mannanase, -arabinosidase, and acetyl esterase. Especially the value of 155 IU · ml^–1 (2,580 nkat ml^–1) for mannanase is remarkable since it appears that this is among the highest activities reported for fungal organisms.Dedicated to Prof. Dr. Robert M. Lafferty on the occasia of his 65th birthday     

Enhanced microbial corrosion of stainless steel by Acidithiobacillus ferrooxidans through the manipulation of substrate oxidation and overexpression of rus

Acidithiobacillus ferrooxidans cells can oxidize iron and sulfur and are key members of the microbial biomining communities that are exploited in the large-scale bioleaching of metal sulfide ores. Some minerals are recalcitrant to bioleaching due to the presence of other inhibitory materials in the ore bodies. Additives are intentionally included in processed metals to reduce environmental impacts and microbially influenced corrosion. We have previously reported a new aerobic corrosion mechanism where A. ferrooxidans cells combined with pyrite and chloride can oxidize low-grade stainless steel (SS304) with a thiosulfate-mediated mechanism. Here we explore process conditions and genetic engineering of the cells that enable corrosion of a higher grade steel (SS316). The addition of elemental sulfur and an increase in the cell loading resulted in a 74% increase in the corrosion of SS316 as compared to the initial sulfur- and cell-free control experiments containing only pyrite. The overexpression of the endogenous rus gene, which is involved in the cellular iron oxidation pathway, led to a further 85% increase in the corrosion of the steel in addition to the improvements made by changes to the process conditions. Thus, the modification of the culturing conditions and the use of rus-overexpressing cells led to a more than threefold increase in the corrosion of SS316 stainless steel, such that 15% of the metal coupons was dissolved in just 2 weeks. This study demonstrates how the engineering of cells and the optimization of their cultivation conditions can be used to discover conditions that lead to the corrosion of a complex metal target.     

Electron transport pathways for the oxidation of endogenous substrate(s) in Acidithiobacillus ferrooxidans

Oxidation of endogenous substrate(s) of Acidithiobacillus ferrooxidans with O2 or Fe3+ as electron acceptor was studied in the presence of uncouplers and electron transport inhibitors. Endogenous substrate was oxidized with a respiratory quotient (CO2 produced/O2 consumed) of 1.0, indicating its carbohydrate nature. The oxidation was inhibited by complex I inhibitors (rotenone, amytal, and piericidin A) only partially, but piericidin A inhibited the oxidation with Fe3+ nearly completely. The oxidation was stimulated by uncouplers, and the stimulated activity was more sensitive to inhibition by complex I inhibitors. HQNO (2-heptyl-4-hydroxyquinoline N-oxide) also stimulated the oxidation, and the stimulated respiration was more sensitive to KCN inhibition than uncoupler stimulated respiration. Fructose, among 20 sugars and sugar alcohols including glucose and mannose, was oxidized with a CO2/O2 ratio of 1.0 by the organism. Iron chelators in general stimulated endogenous respiration, but some of them reduced Fe3+ chemically, introducing complications. The results are discussed in view of a branched electron transport system of the organism and its possible control.     

Interaction of chromosomal and plasmid DNA in Acidithiobacillus ferrooxidans strains adapted to different oxidation substrates

Restriction analysis of plasmids pTFK1 and pTFK2 of the Acidithiobacillus ferrooxidans strain TFBk was carried out, and the sizes of these plasmids were determined (13.5 and 30 kb, respectively). A macrorestriction map was built for plasmid pTFK1. DNA-DNA hybridization revealed that the plasmids contained homologous nucleotide sequences. Plasmid pTFK2 labeled with 32P was used as a probe for Southern hybridization with blots of XbaI-generated fragments of the chromosomal DNA of A. ferrooxidans strains grown on a medium containing Fe2+ or adapted to different oxidation substrates. Low-intensity hybridization signals were observed for many fragments of the chromosomal DNA of the strains studied. In the process of adaptation to new oxidation substrates, the localization of bands producing the low-intensity hybridization signals changed in a number of cases. Certain fragments of the chromosomal DNA of the strains adapted to different oxidation substrates produced strong hybridization signals with pTFK2. The data obtained are discussed in terms of the possible role of IST elements and plasmids in the adaptation of A. ferrooxidans to new energy substrates, microevolution, and strain polymorphism.     

Trace metal optimization in CHO cell culture through statistical design of experiments

A majority of the biotherapeutics industry today relies on the manufacturing of monoclonal antibodies from Chinese hamster ovary (CHO) cells, yet challenges remain with maintaining consistent product quality from high-producing cell lines. Previous studies report the impact of individual trace metal supplemental on CHO cells, and thus, the combinatorial effects of these metals could be leveraged to improve bioprocesses further. A three-level factorial experimental design was performed in fed-batch shake flasks to evaluate the impact of time wise addition of individual or combined trace metals (zinc and copper) on CHO cell culture performance. Correlations among each factor (experimental parameters) and response variables (changes in cell culture performance) were examined based on their significance and goodness of fit to a partial least square's regression model. The model indicated that zinc concentration and time of addition counter-influence peak viable cell density and antibody production. Meanwhile, early copper supplementation influenced late-stage ROS activity in a dose-dependent manner likely by alleviating cellular oxidative stress. Regression coefficients indicated that combined metal addition had less significant impact on titer and specific productivity compared to zinc addition alone, although titer increased the most under combined metal addition. Glycan analysis showed that combined metal addition reduced galactosylation to a greater extent than single metals when supplemented during the early growth phase. A validation experiment was performed to confirm the validity of the regression model by testing an optimized setpoint of metal supplement time and concentration to improve protein productivity.     

Kinetic study of ferrous sulphate oxidation of Acidithiobacillus ferrooxidans in the presence of heavy metal ions

Acidophilic microorganisms such as Acidithiobacillus ferrooxidans have the capability to carry out processes of bioleaching, biosorption and bioprecipitation of heavy metal ions, which have important environmental applications. At. ferrooxidans derives the energy for their metabolism from ferrous iron oxidation, process, which can be affected by the presence of heavy metals in the medium. Moreover, organic matter produces an inhibitory effect over the ferrous iron oxidation of At. ferrooxidans. In this work, heterotrophic bacterium Acidiphilium sp. was added when the medium is supplemented with organic matter to reduce this negative effect. The purpose of this work is the kinetic study of ferrous sulphate oxidation by At. ferrooxidans in the presence of different concentrations of several heavy metal ions (Cr(III), Cu(II), Cd(II), Zn(II) and Ni(II)) and compare this kinetic behaviour with a mixed culture with Acidiphilium sp.The obtained results show a non-competitive inhibition of heavy metals over bacterial oxidation of ferrous sulphate. In accordance with this kind of inhibition, a kinetic equation has been proposed to predict the behaviour of At. ferrooxidans in the presence of heavy metals in the range of concentrations studied.