Metabolomics/Introduction to Metabolomics

Back to Book Table of Contents: Metabolomics Next chapter: Metabolites
 * 1) History
 * 2) Relationship to Traditional Metabolism

The New World of Metabolomics
In the world of biology and biochemistry there are many tiers of function. There is the genome, which is the underlying blueprint for the workings of our cells. From the genome arises the proteome; the factories, building blocks and workhorses of the cell and the organism. But neither of these is enough to truly understand the workings of biological systems.

Cells and organisms have far more in them than just proteins and DNA. Metabolites are the organic chemical compounds that either start off the reactions within biology or act as intermediates, changing or being incorporated into each reaction along a metabolic pathway. The grand total of these compounds and their interactions throughout a cell or a species is the Metabolome. Traditionally metabolism was our way of understanding the Metabolome. It was measured in small-scale pathways through a reductionist approach. The idea was that the sum of the parts could be used to truly understand the whole. But the Metabolome can’t effectively be found through the sum of the parts, especially in the context of systems biology and metabolic engineering.

Newer tiers like Phenomics (the study of the set of phenotypes expressed by a cell) and new disciplines like Nutrigenomics (the study of relationship between nutrition and genetic function) depend heavily on comprehending the Metabolome in a large-scale fashion.

Metabolomics is the solution to this problem. A comprehensive, systems biology conscious approach to understanding the Metabolome in its full scope. Metabolomics seeks to avoid reductionism and apply high throughput analysis methods on metabolic levels in the cell. It will revolutionize fields like metabolic engineering and increase our knowledge of biological function phenomenally.

Recommended Reading & Sources
Introduction: Metabolomics

Peer-Reviewed Article #1:
What is metabolomics all about?

Roessner U, Bowne J. BioTechniques Special Issue (2009) 46:363–365

Reviewer: Arooj I

Main Focus

 * The main focus of “What is metabolic all about?” by Ute Roessner and Jairus Bowne, is to describe various techniques (pathway mapping, metabolite fingerprinting, comparative overlays and etc.) which develop metabolomics to better understand the organization and roles of organisms in the environment. There were four species used in a study to determine the metabolite profiles. These species were; moss Physcomitrella patens, the model plant Arabidopsis thaliana, and the crop plants Hordeum vulgare L. and Triticum aestivum L. These comparisons were done with techniques such as cluster analysis, DiMS, and target analysis.

New Terms
http://www.ajronline.org/cgi/content/full/185/2/299,http://en.wikipedia.org/wiki/Multivariate_statistics < http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCW-3TVXPC7-3&_user=47004&_coverDate=09%2F01%2F1998&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000005018&_version=1&_urlVersion=0&_userid=47004&md5=6ad860575d4269aa5de1da98a652c927>
 * New Term 1: Multi-variant Method: This is a statistical method based on multivariate statistics. Multivariate statistics is a statistical analysis of more than one statistical variable at a time. This technique can be used to detect the effects of all the variables in a trade study.
 * New Term 2: Genetic Perturbation: This is a small change in a physical system. In a genetic perturbation is a biological change such as a mutation in an organism. http://www.ask.com/web?q=dictionary%3A+perturbation&content=ahdict|61997&o=10616&l=dir
 * New Term 3: Metabolome: A metabolome is a complete set of small-molecule metabolites such as metabolic intermediates, hormones and other signaling molecules, and secondary metabolites which can be found within a biological sample, such as a single organism.
 * New Term 4: Transcriptomics: This is the study of a transcriptome. A transcriptome is the complete set of RNA transcripts produced by the genome at any one time. http://www.ask.com/bar?q=What+is+Transcriptomics&page=1&qsrc=2417&dm=all&ab=0&u=http%3A%2F%2Fgenome.wellcome.ac.uk%2Fdoc_WTD020758.html&sg=M6I18%2Fh0XH0FoWssUi2tSOVf6%2FiU%2Fnjmbi36hiDRfOM%3D&tsp=1265598042743
 * New Term 5: Target Analysis: This analysis involves using one particular analytical technique for the determining and quantifying a small set of known metabolites. http://www.jointcommission.org/NR/rdonlyres/2B5D26DA-6BD1-48FD-A7FA-F9BBCBA49A9D/0/ORYX_Target_Analysis.pdf
 * New Term 6: Metabolic Fingerprinting: A mass profile of the sample of interest is generated and then compared in a large sample population to screen for differences between the samples. http://www.biotechniques.com/multimedia/archive/00044/BTN_A_000113133_O_44653a.pdf
 * New Term 7: Direct Infusion Electrospray Mass Spectrometry (DiMS): In this technique, crude extracts of subspecies are taken and directly injected to a mass spectrometer to obtain mass profiles. These mass profiles can then be used to study the metabolite differences between the subspecies of a class.  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC92589/
 * New Term 8: Hierarchical Cluster Analysis: This is a cluster analysis technique which arranges the clusters in an order of hierarchy. The two main categories for the hierarchical arrangements are agglomerative and divisive. Cluster analysis is the assignment of a set of observations into clusters in which the observations have some relevance in relation. http://www.statistics.com/resources/glossary/h/hclusteran.php, http://www.clustan.com/hierarchical_cluster_analysis.html

Summary
Metabolomics in the last twenty years has made gigantic progress in sequencing a number of different organisms and has made large investments in developing analytical approaches for the study of different cell products. These ‘omics approaches such as transcriptomics, metabolomics and etc. are essential in the study of organisms responding to their environments. Metabolomics helps understand the physiological state of an organism. Metabolites act as the language of metabolomics. Only a few technologies have been employed such as mass spectrometry with chromatographic techniques like NMR to analyze these metabolites. Due to the complexity of a metabolome, it is difficult to employ a single technique for analysis. Therefore a number of approaches have to be established for extraction of the information and interpreting it in a biological context. Detection, quantification and identification can be accomplished through cluster analysis, pathway mapping and etc.

One application used in the study of metabolomics is target analysis, which helps in determination and quantification of a few known metabolites. Another application is metabolite profiling which analyzes large set of compounds using important tools like GC-MS. Metabolomics helps quantify as many metabolites as possible and metabolic fingerprinting helps differentiate between these samples.

Most of the research in metabolomics is based on the construction of phylogenetic trees. Primary metabolites are used to determine nutritional and growth status. Secondary metabolites function as markers for taxonomy and phylogenetics. Direct infusion ectecrospray mass spectrometry was a very helpful tool in determining different fungal species. When compared to the phenotypic tree, more than 80% of the species could be classified based on their mass profile. To determine mechanisms for adaptation and tolerance of plants to abiotic stresses revealed that a number of responses are plant specific or are common between stresses and/or plants.

A study to compare levels of metabolites in four different species using metabolomic techniques demonstrated that the metabolite profiles of the species were very different. Classifications such as these demonstrate metabolomics as an important tool for the identification and classification or organisms. Studies in metabolomics would be pretty helpful for the basic principle of life and its evolution. The drawbacks of metabolomics could be that it only measures a small portion of all elements in a biological system. In the future, study of metabolomics such as the response of various organisms to different environments at the genetic, transcript, protein and metabolite levels would strengthen are knowledge of the biology framework in different life systems. It would also help us understand the function, organization and roles of organisms in nature.

Relevance to a Traditional Metabolism Course
The course about metabolism, teaches students about the chemical reactions occurring in an organism such as citric acid cycle, glycolysis and gluconeogenesis. From reading this article, it was found that metabolomics is a study of the chemical footprints left behind by the cellular processes organisms carry out in everyday life. Metabolomics in the article is described by various techniques used to statistically analyze these footprints. The footprints in the article are believed to be called metabolites. These metabolites are studied in subspecies of a class using techniques such as metabolic fingerprinting, DiMS and hierarchical cluster analysis. Most of these techniques are new analytical approaches, allowing biochemists broaden there research goals in metabolism.

Web Resource: Introduction to Metabolomics
Introduction to Metabolomics

[http://plantsci.arabidopsis.info/pg/barratt.pdf Barrett D. Introduction to Metabolomics Powerpoint File. Centre for Analytical Bioscience School of Pharmacy, The University of Nottingam]

Reviewer: Steve S.

Main Focus
A summary of the basic principles of Metabolomics. Serves as a basic introduction to various experimental and analytical techniques of use in the field.

New Terms

 * Genomics: The Study of whole genomes of organisms. Focuses on sequencing and analyzing entire genomes of organisms. (source: http://epa.gov/osa/spc/pdfs/genomics.pdf)
 * Transcriptomics: The Study of gene transcripts. This science involves the study of all types of RNA produced from DNA, mRNA, rRNA, tRNA, and non-coding RNA. The transcript can be from one, or a whole population of cells. (source: http://www.systemsbiology.nl/datgen/transcriptomics/transcriptomics.html)
 * Proteomics: The Study of the final protein products of an organism, population of cells, or individual cell.  Various techniques are used to isolate, identify, and study the proteins in a proteome.(source: http://www.ncbi.nlm.nih.gov/pubmed/9740045)
 * Metabolomics: A field of study regarding the various products and reactions that take place within an organism to achieve its various needs.  Involves the study of both metabolites, as well as metabolic pathways.  Closely associated with the field of proteomics. (source: http://www.bmrb.wisc.edu/metabolomics/)
 * Metabolites: Products, as well as intermediate molecules, involved in metabolism. (source: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1904337/?tool=pubmed)
 * Metabolic Pathway: A set of chemical reactions inside a cell. Through series of intermediate steps,a metabolic pathway provides needed metabolic products.  (source: http://www2.ufp.pt/~pedros/bq/integration.htm)
 * Chromatography: Various laboratory techniqes which involve separating components of a mixture. Include Adsorption, Partition, Ion-exchange, Exclusion, and Affinity chromatography techniques. (source: http://www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf)
 * NMR analysis: Analysis of data aquired through measurement of Nuclear Magnetic Resonance. NMR is a phenomenon that certain nuclei in molecules aquire when exposed to a static magnetic field. This effect is only observed in nuclei that have a property called spin. Through analysis of the level of NMR, information about the contents of a sample can be obtained.  (source: http://www.cis.rit.edu/htbooks/nmr/inside.htm)
 * Metabolomic Fingerprinting: A metabolomic fingerprint is an instantaneous measurement of the biochemistry of a cell under certain conditions. By observing the changes in metabolome under different conditions, these conditions can be diagnosed before typical symptoms occur.   (source: http://dbkgroup.org/dave_files/Pharmacogenomics.pdf)
 * Mass Spectrometry: The determination of chemistry of a molecule by breaking the molecule down into component ions.  These ions are then separated according to their mass, and their charge.  The output of mass spectometry is a count of ions of certain masses/charges. (source: http://www.cem.msu.edu/~reusch/VirtualText/Spectrpy/MassSpec/masspec1.htm)

Summary
Biology can be viewed as information processing on four interconnected levels. Each of these levels of information has an associated field of study. The flow of information starts at DNA, to RNA, to proteins, and finally metabolites. These are studied as the fields of Genomics, Transcriptomics, Proteomics, and Metabolomics. Metabolic Pathways are interconnected sets of chemical reactions. These pathways are complex, and difficult to study. However, many benefits can be gleaned from the study of metabolomics, and metabolites. Many metabolites are very highly conserved molecules. This means that the study of one organism can often yield results applicable to a wide range of organisms. Metabolomes can show influences of both genetics and environmental impacts. This allows metabolic diagnostics to have great power, as regardless of the source of a disease, it can be detected. Metabolites can be analyzed and measured through many techniqes. The main techniques include Mass Spectometry, NMR analysis, and chromatography. There are four levels on which metabolomes can be viewed. From most to least specific, these are Metabolite Target Analysis - measuring specific amounts of a single metabolite, Metabolic Profiling - viewing the abundance of related groups of compounds, metabolomics - the study of all metabolites in a cell, and Metabolic Fingerprinting - simple classification of metabolomes into important categories. There are many contributing factors to the difficulty in studying metabolomes. Rather than processing static information, of specific bits, such as genetics - which are made up of 4 base pairs, or proteins - made up of 20 Amino Acids. In contract, metabolism involves the interactions, over time, of thousands and thousands of different molecules. The products measured for metabolomes can vary in concentration from as low as nanomolar, to micromolar concentrations. Data from metabolomic analysis requires further analysis in order to interpret. The two main forms of these analysis is Principal Component Analysis. Despite these drawbacks, the benefits available from this analysis make it a productive field of study.

Relevance to a Traditional Metabolism Course
This article is a power point presentation, which provides an overview of Metabolomics. It serves nicely as a broad introduction to the techniques available for Metabolomics, as well as the purpose behind these techniques, their strengths, and weaknesses. There is a brief overview as to the role of metabolites, and their position in metabolic pathways - this is mostly presented as a review, however, and is most helpful to one already familiar with the concepts. This article is appropriate for giving an overview, or for a broad review, and does not go in depth in any given topic.