Erich Bornberg-Bauer | |
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| Born | 1963 (age 60–61) Vienna, Austria |
| Nationality | Austrian |
| Alma mater | University of Vienna |
| Known for | |
| Awards | Member Faculty of 1000 |
| Scientific career | |
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| Doctoral advisor | Prof. Peter Schuster |
| Website | bornberglab |
Erich Bornberg-Bauer (born 1963 in Vienna) is an Austrian biochemist, theoretical biologist and bioinformatician.
Bornberg-Bauer, studied biochemistry, physics and mathematics (1981–1991) at the University of Vienna and obtained a diploma in biochemistry (1992). He performed his doctoral research on evolutionary fitness landscapes of RNA and proteins in the group of Peter Schuster, Institute of Theoretical Chemistry, University of Vienna, and received his Ph.D in 1995. [2] He continued his academic career at the University of Vienna (Institute of Mathematics) as a university assistant (equivalent to assistant professor; 1994 – 1996). Thereafter, he worked at the Deutsche Krebsforschungszentrum in Heidelberg as a postdoctoral researcher in the group of Martin Vingron on algorithms for sequence analysis (1996–1998), and subsequently as a project leader at EML (European Media Laboratory) GmbH (1998 – 2000; this department is now a part of Heidelberg Institute for Theoretical Studies). Since 2000, Bornberg-Bauer has been working as an independent academic researcher, first as a senior lecturer in bioinformatics at the University of Manchester (2000–2003), and then as a professor of Molecular Evolution and Bioinformatics at the Institute for Evolution and Biodiversity, University of Münster (2003 – present). [2] Since 2018, he is a guest scientist at the Max Planck Institute for Biology in Tübingen. [3] He has been a guest professor at Claude Bernard University Lyon 1 and a visiting scholar at European Bioinformatics Institute.
Bornberg-Bauer's earlier research focused on the aspects of RNA and protein evolution, especially on the phenomenon of neutral evolution, evolvability and robustness. Together with Hue Sun Chan (University of Toronto), [4] he developed the concept of superfunnels on neutral networks, which describes how populations of functional polymers (such as proteins) randomly explore the sequence space to find transition sequences (switches) to new networks. [5] [6] [7] His work also showed that errors in a protein's sequence that arise during translation (phenotypic mutations), help to explore the sequence space more rapidly. This phenomenon, termed as the look ahead effect, dramatically increases the probability of a gene to acquire beneficial double mutations. [8] His research group at the University of Münster has been working on three main research topics. First is (since 2005) modular evolution of proteins, which involves understanding of how protein domains can reshuffle to create new proteins with altered functions. [2] [9] [10] [11] [12] The second topic is about a phenomenon known as de novo gene birth by which new protein coding genes emerge from DNA segments in an organism's genome, that do not contain any genes. [13] [14] [15] [16] [17] [18] [19] [20] [21] The third topic is genomic analysis of the evolution of eusociality in insects. [22] [23] [24] [25] [26] [27] Bornberg-Bauer has been involved in the initial genome sequencing and annotation of Eucalyptus grandis , [28] Nasonia vitripennis , [29] Nasonia giraulti [29] , Nasonia longicornis , [29] Zostera marina , [30] Bombus terrestris, [31] Bombus impatiens, [31] Atta cephalotes, [32] Blattella germanica [33] and Cryptotermes secundus [33]
His earlier work and most research projects from his group, primarily involve bioinformatics and computational biology. Recent projects form his group have coupled theoretical findings with experiments to understand the molecular evolution of promiscuous (multifunctional) enzymes, [34] and the properties of proteins that emerge de novo. [35] Bornberg-Bauer's work has been supported by the German Research Foundation, the Volkswagen Foundation, the European Commission, and four research grants from the Human Frontier Science Program in 2006, 2013, 2018 and 2023, among others. [2] [36] Since 2021, Bornberg-Bauer is leading the research priority program, "The Genomic Basis of Evolutionary Innovations (GEvol)" of the German Research Foundation [37] [38] [39] He has been Editor-in-chief of Bioinformatics and Biology Insights [40] since 2009 and is editorial member of the Journal of the Royal Society Interface, [41] BMC Evolutionary Biology [42] and the Journal of Experimental Zoology. [43]
Erich Bornberg-Bauer has published more than 150 scientific articles and book chapters.
Scientific articles
Selected publications
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In biology, a mutation is an alteration in the nucleic acid sequence of the genome of an organism, virus, or extrachromosomal DNA. Viral genomes contain either DNA or RNA. Mutations result from errors during DNA or viral replication, mitosis, or meiosis or other types of damage to DNA, which then may undergo error-prone repair, cause an error during other forms of repair, or cause an error during replication. Mutations may also result from insertion or deletion of segments of DNA due to mobile genetic elements.
Molecular evolution describes how inherited DNA and/or RNA change over evolutionary time, and the consequences of this for proteins and other components of cells and organisms. Molecular evolution is the basis of phylogenetic approaches to describing the tree of life. Molecular evolution overlaps with population genetics, especially on shorter timescales. Topics in molecular evolution include the origins of new genes, the genetic nature of complex traits, the genetic basis of adaptation and speciation, the evolution of development, and patterns and processes underlying genomic changes during evolution.
The neutral theory of molecular evolution holds that most evolutionary changes occur at the molecular level, and most of the variation within and between species are due to random genetic drift of mutant alleles that are selectively neutral. The theory applies only for evolution at the molecular level, and is compatible with phenotypic evolution being shaped by natural selection as postulated by Charles Darwin.
Pseudogenes are nonfunctional segments of DNA that resemble functional genes. Most arise as superfluous copies of functional genes, either directly by gene duplication or indirectly by reverse transcription of an mRNA transcript. Pseudogenes are usually identified when genome sequence analysis finds gene-like sequences that lack regulatory sequences needed for transcription or translation, or whose coding sequences are obviously defective due to frameshifts or premature stop codons. Pseudogenes are a type of junk DNA.
Gene duplication is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene. Gene duplications can arise as products of several types of errors in DNA replication and repair machinery as well as through fortuitous capture by selfish genetic elements. Common sources of gene duplications include ectopic recombination, retrotransposition event, aneuploidy, polyploidy, and replication slippage.
In evolutionary biology, conserved sequences are identical or similar sequences in nucleic acids or proteins across species, or within a genome, or between donor and receptor taxa. Conservation indicates that a sequence has been maintained by natural selection.
In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protein-coding genes and non-coding genes.
Directed evolution (DE) is a method used in protein engineering that mimics the process of natural selection to steer proteins or nucleic acids toward a user-defined goal. It consists of subjecting a gene to iterative rounds of mutagenesis, selection and amplification. It can be performed in vivo, or in vitro. Directed evolution is used both for protein engineering as an alternative to rationally designing modified proteins, as well as for experimental evolution studies of fundamental evolutionary principles in a controlled, laboratory environment.
Wen-Hsiung Li is a Taiwanese-American scientist working in the fields of molecular evolution, population genetics, and genomics. He is currently the James Watson Professor of Ecology and Evolution at the University of Chicago and a Principal Investigator at the Institute of Information Science and Genomics Research Center, Academia Sinica, Taiwan.
The MADS box is a conserved sequence motif. The genes which contain this motif are called the MADS-box gene family. The MADS box encodes the DNA-binding MADS domain. The MADS domain binds to DNA sequences of high similarity to the motif CC[A/T]6GG termed the CArG-box. MADS-domain proteins are generally transcription factors. The length of the MADS-box reported by various researchers varies somewhat, but typical lengths are in the range of 168 to 180 base pairs, i.e. the encoded MADS domain has a length of 56 to 60 amino acids. There is evidence that the MADS domain evolved from a sequence stretch of a type II topoisomerase in a common ancestor of all extant eukaryotes.
Orphan genes, ORFans, or taxonomically restricted genes (TRGs) are genes that lack a detectable homologue outside of a given species or lineage. Most genes have known homologues. Two genes are homologous when they share an evolutionary history, and the study of groups of homologous genes allows for an understanding of their evolutionary history and divergence. Common mechanisms that have been uncovered as sources for new genes through studies of homologues include gene duplication, exon shuffling, gene fusion and fission, etc. Studying the origins of a gene becomes more difficult when there is no evident homologue. The discovery that about 10% or more of the genes of the average microbial species is constituted by orphan genes raises questions about the evolutionary origins of different species as well as how to study and uncover the evolutionary origins of orphan genes.
Genome evolution is the process by which a genome changes in structure (sequence) or size over time. The study of genome evolution involves multiple fields such as structural analysis of the genome, the study of genomic parasites, gene and ancient genome duplications, polyploidy, and comparative genomics. Genome evolution is a constantly changing and evolving field due to the steadily growing number of sequenced genomes, both prokaryotic and eukaryotic, available to the scientific community and the public at large.
A circular permutation is a relationship between proteins whereby the proteins have a changed order of amino acids in their peptide sequence. The result is a protein structure with different connectivity, but overall similar three-dimensional (3D) shape. In 1979, the first pair of circularly permuted proteins – concanavalin A and lectin – were discovered; over 2000 such proteins are now known.
A compositional domain in genetics is a region of DNA with a distinct guanine (G) and cytosine (C) G-C and C-G content. The homogeneity of compositional domains is compared to that of the chromosome on which they reside. As such, compositional domains can be homogeneous or nonhomogeneous domains. Compositionally homogeneous domains that are sufficiently long are termed isochores or isochoric domains.
An overlapping gene is a gene whose expressible nucleotide sequence partially overlaps with the expressible nucleotide sequence of another gene. In this way, a nucleotide sequence may make a contribution to the function of one or more gene products. Overlapping genes are present in and a fundamental feature of both cellular and viral genomes. The current definition of an overlapping gene varies significantly between eukaryotes, prokaryotes, and viruses. In prokaryotes and viruses overlap must be between coding sequences but not mRNA transcripts, and is defined when these coding sequences share a nucleotide on either the same or opposite strands. In eukaryotes, gene overlap is almost always defined as mRNA transcript overlap. Specifically, a gene overlap in eukaryotes is defined when at least one nucleotide is shared between the boundaries of the primary mRNA transcripts of two or more genes, such that a DNA base mutation at any point of the overlapping region would affect the transcripts of all genes involved. This definition includes 5′ and 3′ untranslated regions (UTRs) along with introns.
In evolutionary biology, sequence space is a way of representing all possible sequences. The sequence space has one dimension per amino acid or nucleotide in the sequence leading to highly dimensional spaces.
A neutral network is a set of genes all related by point mutations that have equivalent function or fitness. Each node represents a gene sequence and each line represents the mutation connecting two sequences. Neutral networks can be thought of as high, flat plateaus in a fitness landscape. During neutral evolution, genes can randomly move through neutral networks and traverse regions of sequence space which may have consequences for robustness and evolvability.
Zootermopsis nevadensis, the Nevada termite, is a eusocial species of termite (Isoptera) in the family Archotermopsidae, a group known as the dampwood termites. It is a hemimetabolous organism.
Sarah Amalia Teichmann is a German scientist who is head of cellular genetics at the Wellcome Sanger Institute and a visiting research group leader at the European Bioinformatics Institute (EMBL-EBI). She serves as director of research in the Cavendish Laboratory, at the University of Cambridge and a senior research fellow at Churchill College, Cambridge.
De novo gene birth is the process by which new genes evolve from non-coding DNA. De novo genes represent a subset of novel genes, and may be protein-coding or instead act as RNA genes. The processes that govern de novo gene birth are not well understood, although several models exist that describe possible mechanisms by which de novo gene birth may occur.
