293
Views
19
CrossRef citations to date
0
Altmetric
Original Articles

An RNA-Sequencing Study of the Genes and Metabolic Pathways Involved in Aspergillus niger Weathering of Potassium Feldspar

, &
Pages 689-700 | Received 01 Sep 2014, Accepted 01 Nov 2014, Published online: 29 Jun 2015

References

  • Adamo P, Violante P. 2000. Weathering of rocks and neogenesis of minerals associated with lichen activity. Appl Clay Sci 16:229–256.
  • Adeleke RA, Cloete TE, Bertrand A, Khasa DP. 2010. Mobilisation of potassium and phosphorus from iron ore by ectomycorr hizal fungi. World J Microbiol Biotechnol 26:1903–1913.
  • Ademola OA, Geoffrey MG. 2005. Fungal degradation of calcium-, lead-, and silicon-bearing minerals. BioMetals 18:269–281.
  • Andersen MR, Salazar MP, Schaap PJ, van de Vondervoort PJ, Culley D, Thykaer J, Frisvad JC, Nielsen KF, Albang R, Albermann K, Berka RM, Braus GH, Braus-Stromeyer SA, Corrochano LM, Dai Z, van Dijck PW, Hofmann G, Lasure LL, Magnuson JK, Menke H, Meijer M, Meijer SL, Nielsen JB, Nielsen ML, van Ooyen AJ, Pel HJ, Poulsen L, Samson RA, Stam H, Tsang A, van den Brink JM, Atkins A, Aerts A, Shapiro H, Pangilinan J, Salamov A, Lou Y, Lindquist E, Lucas S, Grimwood J, Grigoriev IV, Kubicek CP, Martinez D, van Peij NN, Roubos JA, Nielsen J, Baker SE. 2011. Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 51388. Genome Res 21:885–897.
  • Basak BB, Biswas DR. 2009. Influence of potassium solubilizing microorganism (Bacillus mucilaginosus) and waste mica on potassium uptake dynamics by sudan grass (Sorghum vulgare Pers) grown under two Alfisols. Plant Soil 317:235–255.
  • Beckett GJ, Hayes JD. 1993. Glutathione S-transferases: Biomedical applications. Advan Clin Chem 30:281–380.
  • Bonneville S, Smits MM, Brown A, Harrington J, Leake JR, Brydson R, Benning LG. 2009. Plant-driven fungal weathering: early stages of mineral alteration at the nanometer scale. Geology 37: 615–618.
  • Bublitz M, Poulsen H, Morth JP, Nissen P. 2010. In and out of the cation pumps: P-Type ATPase structure revisited. Curr Opin Struct Biol 20:431–439.
  • Chen J. 2000. Development and utilization of potassium-bearing rock resource and their prospects. Geol Chem Miner 22: 58–64.
  • Chen S, Lian B, Liu CQ. 2008. Effect of Bacillus mucilaginosus on weathering of phosphorite and a preliminary analysis of bacterial proteins. Chin J Geochem 27:209–216.
  • Chou S, Lane S, Liu H. 2006. Regulation of mating and filamentation genes by two distinct Ste12 complexes in Saccharomyces cerevisiae. Mol Cell Biol 26: 4794–805.
  • Cockell CS, Herrera A. 2008. Why are some microorganisms boring? Trends Microbiol 16: 101–106.
  • Du Y, Zhou XY, Lian B. 2008. The extracellular secretion of Bacillus mucilaginosus and its capability of releasing potassium from potassium-bearing minerals. Earth Sci Front 15:107–111.
  • Finlay R, Wallander H, Smits M, Holmstrom S, van Hees P, Lian B. 2009. The role of fungi in biogenic weathering in boreal forest soils. Fung Biol Rev 23:101–106.
  • Griffith OW. 1987. Mammalian sulfur amino acid metabolism: an overview. Meth Enzymol 143:366–376.
  • Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R. 2004. The Gene Ontology (GO) database and informatics resource. Nucl Acids Res 32:D258–D261.
  • Hell R. 1997. Molecular physiology of plant sulfur metabolism. Planta 202:134–138.
  • Hoffland E, Kuyper TW, Wallander H, Plassard C, Gorbushina AA, Haselwandter K, Holmström S, Landeweert R, Lundström US, Rosling A, Sen R, Smits MM, van Hees PAW, van Breemen N. 2004. The role of fungi in weathering. Front Ecol Environ 2:258–264.
  • Hu J, Yu JP, Lian B. 2011a. Capability and mechanism of potassium releasing from potassium-bearing minerals by Aspergillus niger. Bull Mineral Petrol Geochem 30:277–285.
  • Hu J, Lian B, Yu JP, Hu X. 2011b. Formation of Aspergillus niger-mineral aggregation and characterization of polysaccharide from aggregation. Acta Microbiol Sin 51:756–765.
  • Hu X, Lian B, Yu JP, Hu J. 2011c. Effect of potasium-bearing mineral powder on the exo-polysaccharides secreted by Bacillus mucilaginosus. Geol J China Univ 17:107–111.
  • Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y. 2008. KEGG for linking genomes to life and the environment. Nucl Acids Res 36:480–484.
  • Kaur J, Bachhawat AK. 2007. Yct1p, a novel, high-affinity, cysteine-specific transporter from the yeast Saccharomyces cerevisiae. Genetics 176:877–890.
  • Kawahara Y, Oono Y, Kanamori H, Matsumoto T, Itoh T, Minami E. 2012. Simultaneous RNA-Seq analysis of a mixed transcriptome of rice and blast fungus interaction. PLoS ONE 7:e49423.
  • Kredich NM. 1997. Biosynthesis of cysteine In: Neidhardt, FC editors, Escherichia coli and Salmonella: Cellular and Molecular Biology. Washington, DC: American Society for Microbiology, p 514–527.
  • Lee MR, Brown DJ, Smith CL, Hodson ME. 2007. Characterization of mineral surfaces using FIB and TEM: a case study of naturally weathered alkali feldspars Amer Mineral 92:1383–1394.
  • Li FT, Hao ZR, Yang ZY, Zhang CL. 1997. Study on the ability of silicate bactreia HM8841 strain dissolving potassium. Acta Microbiol Sin 37:79–81.
  • Li RQ, Li YR, Fang XD, Yang HM, Wang J, Kristiansen K, Wang J. 2009. SNP detection for massively parallel whole-genome resequencing. Genome Res 19:1124–1132.
  • Lian B, Chen Y, Zhu LJ, Yang RD. 2008a. Effect of microbial weathering on carbonate rocks. Earth Sci Front 15:90–99.
  • Lian B, Fu PQ, Mo DM, Liu CQ. 2002. A comprehensive review of the mechanism of potassium releasing by silicate bacteria. Acta Mineral Sin 22:179–182.
  • Lian B, Wang B, Pan M, Liu CQ, Teng H. 2008b. Microbial release of potassium from K-bearing minerals by thermophilic fungus Aspergillus fumigatus. Geochim Cosmochim Acta 72:87–98.
  • Liu DF, Lian B, Wang B, Jiang GF. 2011. Degradation of potassium rock by earthworms and responses of bacterial communities in its gut and surrounding substrates after being fed with mineral. PLoS ONE 6:e28803.
  • Liu RC, Li FT, Hao ZR, Yang ZY. 1998. The development, research and popularization of biological potassium fertilizer. Scient Agri Sin 31:95–96.
  • Ma HW, Su SQ, Liu H, Yang X, Peng H, Yu ZQ. 2010. Potassium resource and sustainable development of potash salt industry in China. Earth Sci Front 17:294–310.
  • Meister, A. 1988. Glutathione Metabolism and Its Selective Modification. J Biol Chem 263:17205–17208.
  • Mo BB, Lian B. 2010. Study on feldspar weathering and analysis of relevant impact factors. Earth Sci Front 17: 281–289.
  • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold R. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Meth 5:621–628.
  • Nagalakshmi U, Wang Z, Waern K, Chong S, Raha D, Gerstein M, Snyder M. 2008. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320:1344–1349.
  • Olsson-Francis K, Houdt RV, Mergeay M, Leys N, Cockell, CS. 2010. Microarray analysis of a microbe-mineral interaction. Geobiology 8:446–456.
  • Ono BI, Hazu T, Yoshida S, Kawato T, Shinoda S, Brzywczy J. 1999. Cysteine biosynthesis in Saccharomyces cerevisiae: a new outlook on pathway and regulation. Yeast 15:1365–1375.
  • Pel HJ, De Winde JH, Archer DB, Dyer PS, Hofmann G, Schaap PJ, Turner G, de Vries RP, Albang R, Albermann K, Andersen MR, Bendtsen JD, Benen JA, van den Berg M, Breestraat S, Caddick MX Contreras R, Cornell M, Coutinho PM, Danchin EG, Debets AJ, Dekker P, van Dijck PW, van Dijk A, Dijkhuizen L, Driessen AJ, d′Enfert C, Geysens S, Goosen C, Groot GS, de Groot PW, Guillemette T, Henrissat B, Herweijer M, van den Hombergh JP, van den Hondel CA, van der Heijden RT, van der Kaaij RM, Klis FM, Kools HJ, Kubicek CP, van Kuyk PA, Lauber J, Lu X, van der Maarel MJ, Meulenberg R, Menke H, Mortimer MA, Nielsen J, Oliver SG, Olsthoorn M, Pal K, van Peij NN, Ram AF, Rinas U, Roubos JA, Sagt CM, Schmoll M, Sun J, Ussery D, Varga J, Vervecken W, van de Vondervoort PJ, Wedler H, Wösten HA, Zeng AP, van Ooyen AJ, Visser J, Stam H. 2007. Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 51388. Nat Biotechnol 25: 221–231.
  • Qiu SS, Lian B. 2012. Weathering of phosphorus-bearing mineral powder and calcium phosphate by Aspergillus niger. Chin J Geochem 31:390–397.
  • Riccombeni A, Butler G. 2012. Role of genomics and RNA-seq in studies of fungal virulence. Curr Fung Infect Repts 6: 267–274.
  • Richards FM, Kundrot CE. 1988. Identification of structural motifs from protein coordinate data: secondary structure and first-level supersecondary structure. Proteins 3:71–84.
  • Sun LL, Lian B, Xiao LL, Xiao B, Wang WY, Pan C, Wang SJ, Lian B. 2013. Differences in the gene expressive quantities of carbonic anhydrase and cysteine synthase in the weathering of potassium-bearing minerals by Aspergillus niger. Sci China: Earth Sci 56:1–6.
  • Uroz S, Calvaruso C, Turpault MP, Frey-Klett P. 2009. Mineral weathering by bacteria: ecology, actors and mechanisms. Trends Microbiol 17:378–387.
  • Wallander H, Hagerberg D. 2004. Do ectomycorrhizal fungi have a significant role in weathering of minerals in forest soil? Symbiosis 37:249–257.
  • Wang B, Guo GW, Wang C, Lin Y. 2010. Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing. Nucl Acids Res 38:5075–5087.
  • Wang WJ, Bai ZM, Ma HW. 1996. Developments and prospects of extracting potash from insoluble potash ores. Geol Sci Technol Info 15:59–63.
  • Wang B, Guo GW, Wang C, Lin Y, Wang XN, Zhao MM, Guo Y, He MH, Zhang Y, Pan L. 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63.
  • Welch SA, Ullman WJ. 1993. The effect of organic acids on plagioclase dissolution rates and stoichiometry. Geochim Cosmochim Acta 57:2725–2736.
  • Wu WS, Li WH. 2008. Systematic identification of yeast cell cycle transcription factors using multiple data sources. BMC Bioinformatics 9:522.
  • Xiao LL, Hao JC, Wang WY, Lian B, Shang GD, Yang YW, Liu CQ, Wang SJ. 2014. The up-regulation of carbonic anhydrase genes of Bacillus mucilaginosus under soluble Ca2+ deficiency and the heterologously expressed enzyme promotes calcite dissolution. Geomicrobiol J 31:632–641.
  • Xiao B, Lian B, Shao WL. 2012a. Do bacterial secreted proteins play a role in the weathering of potassium-bearing rock powder? Geomicrobiol J 29:497–505.
  • Xiao B, Lian B, Sun LL, Shao WL, Shang GD, Yang YW, Liu CQ, Wang SJ. 2012b. Gene transcription response to weathering of K-bearing minerals by Aspergillus fumigatus. Chem Geol 306:1–9.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.