73
© The Author(s) 2018
S. Jungblut et al. (eds.), YOUMARES 8 – Oceans Across Boundaries: Learning from each other,
https://doi.org/10.1007/978-3-319-93284-2_6
Reading the Book of Life – Omics
as a Universal Tool Across Disciplines
Jan David Brüwer and Hagen Buck-Wiese
Abstract
In the last centuries, new high-throughput technologies,
including sequencing and mass-spectrometry, have
emerged and are constantly refurbished in order to decipher the molecular code of life. In this review, we summarize the physiological background from genes via
transcriptome to proteins and metabolites and discuss the
variety of dimensions in which a biological entity may be
studied. Herein, we emphasize regulatory processes
which underlie the plasticity of molecular profiles on different ome layers. We discuss the four major fields of
omic research, namely genomics, transcriptomics, proteomics, and metabolomics, by providing specific examples and case studies for (i) the assessment of functionality
on molecular, organism, and community level; (ii) the
possibility to use omic research for categorization and
systematic efforts; and (iii) the evaluation of responses to
environmental cues with a special focus on anthropogenic
influences. Thereby, we exemplify the knowledge gains
attributable to the integration of information from different omes and the enhanced precision in predicting the
phenotype. Lastly, we highlight the advantages of combining multiple omics layers in assessing the complexity
of natural systems as meta-communities and -organisms.
Introduction and Historical Background
The discovery of nucleic acids in 1896 by Friedrich Miescher
and the suggestion of deoxyribonucleic acid (DNA) as the
genetic material by Avery, MacLeod, and McCarty in 1943
revolutionized the life sciences (Avery et al. 1943; Dahm
2005). Genomics, from the suggested word “genome” for
haploid chromosome sets by Hans Winkler (Noguera-Solano
et al. 2013), arose with the aim to decipher the molecular
language. It took another 10 years before Franklin, Wilkins,
Watson, and Crick unraveled the double-helical structure of
DNA in 1953 (Dahm 2005). The conversion from nucleotide
sequence into amino acid was first recognized, when
Heinrich Matthaei and Marshall Nirenberg discovered that
the RNA sequence of three Uracil bases codes for the amino
acid phenylalanine with their so-called Poly-U experiment
(Nirenberg 2004; Dahm 2005). Five years later, in 1966, the
translation of all base combinations into the 20 proteinforming amino acids had been resolved (Nirenberg 2004).
For nucleotide sequence analysis, Frederick Sanger and colleagues developed the first widely applied method, the
Sanger sequencing, in 1977 and, thus, established the foundation for modern genomic and transcriptomic research
(Box 1) (Sanger et al. 1977). In more recent years, highthroughput molecular technologies, e.g., next-generation
sequencing (NGS) (Box 1) and mass spectrometry (Box 2)
have developed, enabling genome-scale deciphering of the
molecular signatures, which encode life on earth.
These technologies provide the opportunity for a wide
range of studies which can be divided into four major fields
according to the targeted molecules: genomics, transcriptomics, proteomics, and metabolomics. In definition, genomics describes the analysis of any genetic material (DNA)
isolated from an organism or the environment. It includes,
for example, whole genome sequencing and detection methods such as environmental DNA (eDNA). Transcriptomics is
the study of any form of RNA, including messenger RNA
(mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA),
J. D. Brüwer (*)
Red Sea Research Center, Division of Biological and
Environmental Science and Engineering (BESE), King Abdullah
University of Science and Technology (KAUST),
Thuwal, Saudi Arabia
Faculty of Biology and Chemistry, University of Bremen,
Bremen, Germany
Max Planck Institute for Marine Microbiology, Bremen, Germany
e-mail: bruewer_j@gmx.de
H. Buck-Wiese (*)
Faculty of Biology and Chemistry, University of Bremen,
Bremen, Germany
Max Planck Institute for Marine Microbiology, Bremen, Germany
e-mail: h.buckwiese@googlemail.com
© The Author(s) 2018
S. Jungblut et al. (eds.), YOUMARES 8 – Oceans Across Boundaries: Learning from each other,
https://doi.org/10.1007/978-3-319-93284-2_6
Reading the Book of Life – Omics
as a Universal Tool Across Disciplines
Jan David Brüwer and Hagen Buck-Wiese
Abstract
In the last centuries, new high-throughput technologies,
including sequencing and mass-spectrometry, have
emerged and are constantly refurbished in order to decipher the molecular code of life. In this review, we summarize the physiological background from genes via
transcriptome to proteins and metabolites and discuss the
variety of dimensions in which a biological entity may be
studied. Herein, we emphasize regulatory processes
which underlie the plasticity of molecular profiles on different ome layers. We discuss the four major fields of
omic research, namely genomics, transcriptomics, proteomics, and metabolomics, by providing specific examples and case studies for (i) the assessment of functionality
on molecular, organism, and community level; (ii) the
possibility to use omic research for categorization and
systematic efforts; and (iii) the evaluation of responses to
environmental cues with a special focus on anthropogenic
influences. Thereby, we exemplify the knowledge gains
attributable to the integration of information from different omes and the enhanced precision in predicting the
phenotype. Lastly, we highlight the advantages of combining multiple omics layers in assessing the complexity
of natural systems as meta-communities and -organisms.
Introduction and Historical Background
The discovery of nucleic acids in 1896 by Friedrich Miescher
and the suggestion of deoxyribonucleic acid (DNA) as the
genetic material by Avery, MacLeod, and McCarty in 1943
revolutionized the life sciences (Avery et al. 1943; Dahm
2005). Genomics, from the suggested word “genome” for
haploid chromosome sets by Hans Winkler (Noguera-Solano
et al. 2013), arose with the aim to decipher the molecular
language. It took another 10 years before Franklin, Wilkins,
Watson, and Crick unraveled the double-helical structure of
DNA in 1953 (Dahm 2005). The conversion from nucleotide
sequence into amino acid was first recognized, when
Heinrich Matthaei and Marshall Nirenberg discovered that
the RNA sequence of three Uracil bases codes for the amino
acid phenylalanine with their so-called Poly-U experiment
(Nirenberg 2004; Dahm 2005). Five years later, in 1966, the
translation of all base combinations into the 20 proteinforming amino acids had been resolved (Nirenberg 2004).
For nucleotide sequence analysis, Frederick Sanger and colleagues developed the first widely applied method, the
Sanger sequencing, in 1977 and, thus, established the foundation for modern genomic and transcriptomic research
(Box 1) (Sanger et al. 1977). In more recent years, highthroughput molecular technologies, e.g., next-generation
sequencing (NGS) (Box 1) and mass spectrometry (Box 2)
have developed, enabling genome-scale deciphering of the
molecular signatures, which encode life on earth.
These technologies provide the opportunity for a wide
range of studies which can be divided into four major fields
according to the targeted molecules: genomics, transcriptomics, proteomics, and metabolomics. In definition, genomics describes the analysis of any genetic material (DNA)
isolated from an organism or the environment. It includes,
for example, whole genome sequencing and detection methods such as environmental DNA (eDNA). Transcriptomics is
the study of any form of RNA, including messenger RNA
(mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA),
J. D. Brüwer (*)
Red Sea Research Center, Division of Biological and
Environmental Science and Engineering (BESE), King Abdullah
University of Science and Technology (KAUST),
Thuwal, Saudi Arabia
Faculty of Biology and Chemistry, University of Bremen,
Bremen, Germany
Max Planck Institute for Marine Microbiology, Bremen, Germany
e-mail: bruewer_j@gmx.de
H. Buck-Wiese (*)
Faculty of Biology and Chemistry, University of Bremen,
Bremen, Germany
Max Planck Institute for Marine Microbiology, Bremen, Germany
e-mail: h.buckwiese@googlemail.com