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Comparative Genomic Analysis of Carbon and Nitrogen Assimilation BMC Genomics BioMed Central Research article Open Access Comparative genomic analysis of carbon and nitrogen assimilation mechanisms in three indigenous bioleaching bacteria: predictions and validations Gloria Levicán†1,4, Juan A Ugalde†2,5, Nicole Ehrenfeld1,6, Alejandro Maass2,3 and Pilar Parada*1 Address: 1Biosigma 'S.A.', Loteo Los Libertadores, Lote 106, Colina, Chile, 2Laboratory of Bioinformatics and Mathematics of the Genome, Center for Mathematical Modeling, Faculty of Mathematical and Physical Sciences, Avda Blanco Encalada 2120, 7th Floor, University of Chile, Santiago, Chile, 3Department of Mathematical Engineering and Center for Mathematical Modeling (UMI 2807, CNRS), Faculty of Mathematical and Physical Sciences, Avda Blanco Encalada 2120, 7th Floor, University of Chile, Santiago, Chile, 4Biology Department, Chemistry and Biology Faculty, University of Santiago of Chile, Avda. Libertador Bernardo O'Higgins 3363, Estación Central, Santiago, Chile, 5Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093-0208, USA and 6Austral Biotech, Francisco Noguera 41, Piso 3, Providencia, Santiago, Chile Email: Gloria Levicán - [email protected]; Juan A Ugalde - [email protected]; Nicole Ehrenfeld - [email protected]; Alejandro Maass - [email protected]; Pilar Parada* - [email protected] * Corresponding author †Equal contributors Published: 3 December 2008 Received: 11 August 2008 Accepted: 3 December 2008 BMC Genomics 2008, 9:581 doi:10.1186/1471-2164-9-581 This article is available from: http://www.biomedcentral.com/1471-2164/9/581 © 2008 Levicán et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Carbon and nitrogen fixation are essential pathways for autotrophic bacteria living in extreme environments. These bacteria can use carbon dioxide directly from the air as their sole carbon source and can use different sources of nitrogen such as ammonia, nitrate, nitrite, or even nitrogen from the air. To have a better understanding of how these processes occur and to determine how we can make them more efficient, a comparative genomic analysis of three bioleaching bacteria isolated from mine sites in Chile was performed. This study demonstrated that there are important differences in the carbon dioxide and nitrogen fixation mechanisms among bioleaching bacteria that coexist in mining environments. Results: In this study, we probed that both Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans incorporate CO2 via the Calvin-Benson-Bassham cycle; however, the former bacterium has two copies of the Rubisco type I gene whereas the latter has only one copy. In contrast, we demonstrated that Leptospirillum ferriphilum utilizes the reductive tricarboxylic acid cycle for carbon fixation. Although all the species analyzed in our study can incorporate ammonia by an ammonia transporter, we demonstrated that Acidithiobacillus thiooxidans could also assimilate nitrate and nitrite but only Acidithiobacillus ferrooxidans could fix nitrogen directly from the air. Conclusion: The current study utilized genomic and molecular evidence to verify carbon and nitrogen fixation mechanisms for three bioleaching bacteria and provided an analysis of the potential regulatory pathways and functional networks that control carbon and nitrogen fixation in these microorganisms. Page 1 of 19 (page number not for citation purposes) BMC Genomics 2008, 9:581 http://www.biomedcentral.com/1471-2164/9/581 Background gen. Ammonium, nitrate, nitrite and glutamine are the The employment of microorganisms for metal recovery main nitrogen sources used by microorganisms in natural from low-grade ores and mineral concentrates and sec- environments. Under low nitrogen levels, diazotrophic ondary materials, has developed into a successful and bacteria can fix atmospheric nitrogen under anaerobic or expanding area of biotechnology. In association with this microaerobic conditions through the action of the nitro- interest, microbial communities of extreme acidophilic genase complex. Because reduction of N2 to ammonium is prokaryotes from bioleaching environments have long an energy-demanding process and because the nitroge- been the subject of active research; however, the compo- nase enzyme is very sensitive to oxygen, biological N2 nents and interactions within these microbial communi- reduction is a tightly regulated process [18,19]. ties' remains poorly understood. Recent acquisition of genomic data directly from organisms living in naturally The capability of microorganisms to fix atmospheric extreme environments [1-4] in combination with genome nitrogen plays an important role in recycling scarce nitro- sequencing projects of individual species [5,6] provides a gen existing in nutrient-poor acidic conditions; however, novel opportunity for prediction and exploration of the the availability of nitrogen and the energy required for its metabolic details that control both individual microor- fixation may limit bacterial growth and adversely affect ganisms and microorganism communities. the efficiency of bioleaching operations. The study of nitrogen metabolism in members of microbial communi- Acidophilic prokaryotes involved in metal recovery from ties is therefore of both fundamental and applied interest. sulfide minerals include members of the Bacteria and In bioleaching communities N2 fixation has been pre- Archaea domains. Three species of chemolithotrophic dicted for A. ferrooxidans [5,20-22] and members of bacteria are mainly involved: Acidithiobacillus ferrooxidans, groups I [23,4] and III [24] of the Leptospirillum genus. Acidithiobacillus thiooxidans and Leptospirillum sp., all of Genomic analysis of these bacteria revealed the presence which obtain energy primarily from iron and/or sulfur of genes involved in N2 fixation (nif), ammonium trans- oxidation. A. ferrooxidans is capable of oxidizing reduced port (amt) and genes encoding the regulatory proteins sulfur compounds and Fe2+ ions to form sulfate and Fe3+, NtrC and NifA (specific activators of nif genes). Genes respectively [7-10]. A. thiooxidans can only oxidize encoding the regulatory PII protein, which plays a con- reduced sulfur compounds such as thiosulfate, tetrathion- trolling role in the nitrogen metabolism coupled to the ate, metal sulfides and elemental sulfur to form sulfate [7- central carbon metabolism [25,26], have also been identi- 9,11]. Leptospirillum sp. is solely capable of oxidizing Fe2+ fied. ions to form Fe3+ [12]. These autotrophic microorganisms utilize the energy and reducing power derived from iron Although carbon and nitrogen fixation has been predicted and/or sulfur oxidation for several metabolic processes, for A. ferrooxidans and members of the Leptospirillum including CO2 fixation and acquisition of several sources genus, the physiology and regulation of these processes of nitrogen. In both Acidithiobacillus species, CO2 fixation are still poorly understood. Here we report a comparative occurs via the Calvin-Benson-Bassham cycle [5,13,14] genomic analysis of the carbon and nitrogen metabolism whereas Leptospirillum sp. grows autotrophically; however carried out on three sequenced bacterial genomes (A. fer- the molecular mechanisms involved in carbon fixation rooxidans, A. thiooxidans and Leptospirillum group II) iso- remain obscure. lated from naturally extreme environments in the north of Chile. In acidic bioleaching environments, dissolved inorganic carbon can reach levels below atmospheric concentra- Results and discussion tions average. Therefore, it is not surprising that CO2 con- Molecular mechanisms involved in CO2 fixation centrating mechanisms have been identified in CO2 fixation by the Calvin-Benson-Bassham (CBB) cycle autotrophic prokaryotes present in such environments CBB is composed of 13 enzymatic reactions, 12 of which [15,16]. In A. ferrooxidans (ATCC 23270), the presence of are involved in regeneration of ribulose 1,5-bisphosphate carboxysomes has been inferred from genome annotation (RuBP) and one of which is responsible for CO2 fixation [17], but the physiological role of this compartment and catalyzed by ribulose 1,5-bisphosphate carboxylase/oxy- characterization of global CO2 concentrating mechanisms genase (Rubisco). The key CO2 fixation enzymes in the in bioleaching bacteria are yet to be determined. CBB cycle are Rubisco, Phosphoribulokinase (PRK) and Sedoheptulose 1,7-bisphosphatase (SBP) [27]. We Nitrogen plays an important role in the ecology of micro- searched in the genomes of Acidithiobacillus ferrooxidans, bial communities. Therefore, understanding the molecu- Acidithiobacillus thiooxidans and Leptospirillum ferriphilum lar mechanisms involved in nitrogen fixation and for genes encoding these CBB enzymes (See additional file assimilation are critical to understand how microorgan- 1: CarbAsilProts.csv for the list and sequence of these pro- isms adapt themselves to changes in environmental nitro- teins). PRK and SBP genes were identified in the Acidithio- Page 2 of 19 (page number not for citation purposes) BMC Genomics 2008, 9:581 http://www.biomedcentral.com/1471-2164/9/581 bacillus strains as single copies but not in the Leptospirillum doreductase (OGOR) and pyruvate ferredoxin oxidore- strain. We identified canonical
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