Metabolic reconstruction of sulfur assimilation in the extremophile Acidithiobacillus ferrooxidans based on genome analysis

Valdés, Jorge; Veloso, Felipe; Jedlicki, Eugenia; Holmes, David
January 2003
BMC Genomics;2003, Vol. 4, p1
Academic Journal
Background: Acidithiobacillus ferrooxidans is a gamma-proteobacterium that lives at pH2 and obtains energy by the oxidation of sulfur and iron. It is used in the biomining industry for the recovery of metals and is one of the causative agents of acid mine drainage. Effective tools for the study of its genetics and physiology are not in widespread use and, despite considerable effort, an understanding of its unusual physiology remains at a rudimentary level. Nearly complete genome sequences of A. ferrooxidans are available from two public sources and we have exploited this information to reconstruct aspects of its sulfur metabolism. Results: Two candidate mechanisms for sulfate uptake from the environment were detected but both belong to large paralogous families of membrane transporters and their identification remains tentative. Prospective genes, pathways and regulatory mechanisms were identified that are likely to be involved in the assimilation of sulfate into cysteine and in the formation of Fe-S centers. Genes and regulatory networks were also uncovered that may link sulfur assimilation with nitrogen fixation, hydrogen utilization and sulfur reduction. Potential pathways were identified for sulfation of extracellular metabolites that may possibly be involved in cellular attachment to pyrite, sulfur and other solid substrates. Conclusions: A bioinformatic analysis of the genome sequence of A. ferrooxidans has revealed candidate genes, metabolic process and control mechanisms potentially involved in aspects of sulfur metabolism. Metabolic modeling provides an important preliminary step in understanding the unusual physiology of this extremophile especially given the severe difficulties involved in its genetic manipulation and biochemical analysis.


Related Articles

  • A Computational Approach to the Functional Screening of Genomes. Chiarugi, Davide; Degano, Pierpaolo; Marangoni, Roberto // PLoS Computational Biology;Sep2007, Vol. 3 Issue 9, p1801 

    Comparative genomics usually involves managing the functional aspects of genomes, by simply comparing gene-by- gene functions. Following this approach, Mushegian and Koonin proposed a hypothetical minimal genome, Minimal Gene Set (MGS), aiming for a possible oldest ancestor genome. They obtained...

  • Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701) and emended description of the genus Thermanaerovibrio. Palaniappan, Krishna; Meier-Kolthoff, Jan; Teshima, Hazuki; Nolan, Matt; Lapidus, Alla; Tice, Hope; Glavina Del Rio, Tijana; Cheng, Jan-Fang; Han, Cliff; Tapia, Roxanne; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Mavromatis, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Rohde, Manfred // Standards in Genomic Sciences;Jul2013, Vol. 9 Issue 1, p57 

    Thermanaerovibrio velox Zavarzina et al. 2000 is a member of the Synergistaceae, a family in the phylum Synergistetes that is already well-characterized at the genome level. Members of this phylum were described as Gram-negative staining anaerobic bacteria with a rod/vibrioid cell shape and...

  • Phylogenetic signal and functional categories in Proteobacteria genomes. Comas, Iñaki; Moya, Andrés; González-Candelas, Fernando // BMC Evolutionary Biology;2007 Supplement 1, Vol. 7, pS7 

    Background: A comprehensive evolutionary analysis of bacterial genomes implies to identify the hallmark of vertical and non-vertical signals and to discriminate them from the presence of mere phylogenetic noise. In this report we have addressed the impact of factors like the universal...

  • Three factors underlying incorrect in silico predictions of essential metabolic genes. Becker, Scott A.; Palsson, Bernhard O. // BMC Systems Biology;2008, Vol. 2, Special section p1 

    Background: The indispensability of certain genes in an organism is important for studies of microorganism physiology, antibiotic targeting, and the engineering of minimal genomes. Time and resource intensive genome-wide experimental screens can be conducted to determine which genes are likely...

  • Metabolism: Digging up enzyme functions. Wargo, Matthew J // Nature Chemical Biology;Jan2014, Vol. 10 Issue 1, p4 

    The article presents information on a study related to the functions of cryptic bacterial enzymes with the help of genome sequencing and structural biology methods. It informs that the one need to know which genes are expressed and the functions of the proteins those genes encode. It also...

  • Metabolic fluxes and beyond-systems biology understanding and engineering of microbial metabolism. Kohlstedt, Michael; Becker, Judith; Wittmann, Christoph // Applied Microbiology & Biotechnology;Nov2010, Vol. 88 Issue 5, p1065 

    The recent years have seen tremendous progress towards the understanding of microbial metabolism on a higher level of the entire functional system. Hereby, huge achievements including the sequencing of complete genomes and efficient post-genomic approaches provide the basis for a new,...

  • Transcript analysis of the Halothiobacillus neapolitanus cso operon. Fei Cai; Heinhorst, Sabine; Shively, Jessup M.; Cannon, Gordon C. // Archives of Microbiology;Feb2008, Vol. 189 Issue 2, p141 

    Carboxysomes are polyhedral microcompartments that sequester the CO2-fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase in many autotrophic bacteria. Their protein constituents are encoded by a set of tightly clustered genes that are thought to form an operon (the cso operon). This...

  • Insight into the Sulfur Metabolism by Thermoacidophilic Archaeon Metallosphaera Cuprina with Genomic, Proteomic and Biochemical Tools. Jin-Long Song; Cheng-Ying Jiang; Shuang-Jiang Liu // Advanced Materials Research;2015, Vol. 1130, p145 

    The thermoacidophilic archaeon Metallosphaera cuprina was isolated from a sulfuric hot spring. M. cuprina is able to oxidize elemental sulfur, tetrathionate (S4O62+) pyrite, and a range of low-grade ores, thus is attractive to biomining industry. Dissimilatory sulfur metabolism with a oxygenase...

  • Isolation and characterization of a gene associated with sulfate assimilation in Sinorhizobium fredii WGF03. Song, Zhangyang; Shen, Peihong; Ma, Tingting; Jiang, Chengjian; Zhao, Huaxian; Wu, Bo // World Journal of Microbiology & Biotechnology;Dec2014, Vol. 30 Issue 12, p3027 

    Sulfur is an essential element for rhizobia, such as sulfated modified Nod factors and nitrogenase. To investigate the role of sulfur metabolism in Rhizobium-Soybean symbiosis, a transponson random insertional mutants' library was constructed and a sulfur assimilation-related gene was isolated...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics