title: A universal protocol for the combined isolation of metabolites, DNA, long RNAs, small RNAs, and proteins from plants and microorganisms.
abstract: Here, we describe a method for the combined metabolomic, proteomic, transcriptomic and genomic analysis from one single sample as a major step for multilevel data integration strategies in systems biology. While extracting proteins and DNA, this protocol also allows the separation of metabolites into polar and lipid fractions, as well as RNA fractionation into long and small RNAs, thus allowing a broad range of transcriptional studies. The isolated biomolecules are suitable for analysis with different methods that range from electrophoresis and blotting to state-of-the-art procedures based on mass spectrometry (accurate metabolite profiling, shot-gun proteomics) or massive sequencing technologies (transcript analysis). The low amount of starting tissue, its cost-efficiency compared with the utilization of commercial kits, and its performance over a wide range of plant, microbial, and algal species such as Chlamydomonas, Arabidopsis, Populus, or Pinus, makes this method a universal alternative for multiple molecular isolation from plant tissues.
authors.affiliation: Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal; Global Change Research Centre-Czechglobe, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
authors.forename: Luis
authors.initials: L
authors.lastname: Valledor
authors.forename: Mónica
authors.initials: M
authors.lastname: Escandón
authors.forename: Mónica
authors.initials: M
authors.lastname: Meijón
authors.forename: Ella
authors.initials: E
authors.lastname: Nukarinen
authors.forename: María Jesús
authors.initials: MJ
authors.lastname: Cañal
authors.forename: Wolfram
authors.initials: W
authors.lastname: Weckwerth
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D016825:Chlamydomonas reinhardtii / Q000235:genetics / Q000378:metabolism; D018744:DNA, Plant / Q000302:isolation & purification*; D023281:Genomics / Q000379:methods; D055432:Metabolomics / Q000379:methods; D028223:Pinus / Q000235:genetics / Q000378:metabolism; D010940:Plant Proteins / Q000302:isolation & purification*; D010944:Plants / Q000235:genetics / Q000378:metabolism; D032107:Populus / Q000235:genetics / Q000378:metabolism; D040901:Proteomics / Q000379:methods; D018749:RNA, Plant / Q000302:isolation & purification*; D015203:Reproducibility of Results; D049490:Systems Biology / Q000379:methods*
chemical_list: D018744:DNA, Plant; D010940:Plant Proteins; D018749:RNA, Plant
keywords: Arabidopsis thaliana; Chlamydomonas reinhardtii; Pinus sp.; Populus sp.; RNA; combined isolation; metabolites; proteins; small RNA; systems biology; technical advance