Biology subjects

Bornberg-Bauer, E.

Publications and source records attributed to Bornberg-Bauer, E..

At least 19 recordsLinked to original sources

bioRxiv2026

How are evolutionarily young and old proteins distributed in sequence space?

Protein sequence space is vast due to the combinatorial diversity of 20 amino acids. However, evolution has generated a limited set of "old" canonical protein families sharing evolutionary ancestry, structures and functions. It remains unclear how canonical sequences are placed in sequence space, how recently evolved "young" proteins compare to them, and whether random, young, and canonical sequences can interconvert along evolutionarily plausible paths, and which biophysical properties distinguish or link these sequences. Here, we analyse naturally occurring de novo proteins from yeast and flies, which originate from non-coding DNA and thus have experienced limited evolutionary selection. They serve as a model for examining the relationships between young de novo and intergenic proteins, older canonical proteins, and their randomized counterparts. Because de novo and randomized sequences lack detectable homology, we use an alignment-free k-mer-based distance approach. Randomization shifts distance distributions toward expected random behaviour in all classes, but natural, non-randomized sequence classes remain distinct, indicating non-random residue organization. Each class exhibits characteristic k-mer patterns, with de novo proteins clearly separated from both canonical and all randomized sequences. Sequences bridging these classes are frequently predicted to contain transmembrane helices. De novo proteins are thus not random samples of sequence space. Instead, they occupy constrained yet evolutionarily accessible regions defined by residue order and biophysical constraints, suggesting a plausible pathway for the emergence and diversification of new proteins. Significance StatementDespite the vast combinatorial potential of amino acids, evolution has produced only a limited repertoire of canonical proteins with conserved structure and function. How evolutionarily young proteins relate to older canonical proteins, and whether the sequence space between them is traversable, remain unclear. Here, we decompose canonical proteins, intergenic sequences, and recently emerged yeast and fly de novo proteins, together with randomized controls, into short, interpretable fragments (k-mers) and compare them using alignment-free distances. De novo proteins are markedly distinct from both randomized and canonical sequences. Notwithstanding their evolutionary distance, sequences are connected by stepwise paths comprising bridge sequences, often enriched for low-complexity motifs and transmembrane helices, connecting disordered and structured regions of sequence space.

evolutionary biology↗

bioRxiv2026

Structure can emerge from disorder under neutral evolution

Mutations are often thought to destabilize protein structures. However, many proteins are naturally unstructured and the effect of mutations on such proteins especially in the absence of selection, remains unclear. Here, we develop a computational model to study the effects of mutations on structural disorder in both random and natural sequences, including those derived from evolutionary conserved proteins, and evolutionarily novel de novo proteins. We find that while structured proteins tend to lose structure, unstructured proteins exhibit the opposite trend, becoming more structured in the absence of directional selection. This bidirectional dynamics is robust to mutation biases, genetic code structure, and sequence origin, suggesting that it arises from the topology of the sequence-structure landscape rather than intrinsic directional mechanisms. Our results are consistent with a diffuse landscape in which structured and disordered sequences are interspersed throughout sequence space. These findings suggest that neutral evolution can result in structure formation and may facilitate the early structural evolution of de novo proteins prior to strong selection.

evolutionary biology↗

bioRxiv2025

Pervasive translation of short open reading frames and de novo gene emergence in Arabidopsis

Ancestrally non-genic sequences are now widely recognized as potential reservoirs for the de novo emergence of new genes. Across clades, some de novo genes were proven to have substantial phenotypic effects, and to contribute to the emergence of novel biological functions. Yet, little is still known about the starting material from which de novo genes emerge, especially in plants. To fill this gap, we generated Ribosome Profiling data from Arabidopsis lyrata and characterized the evolution of translated regions genome-wide across the Arabidopsis genus. Synteny analysis revealed 163 actively translated regions in A. lyrata whose coding potential (Open Reading Frames, ORFs or Coding DNA sequences, CDSs) has emerged de novo within the Arabidopsis genus. Most of these de novo translated regions were species- and even accession-specific, indicating their transient nature, with patterns of polymorphism consistent with neutral evolution in natural populations. They were also significantly shorter and less expressed than conserved protein-coding genes, and their GC content increased with phylogenetic conservation. Twenty-one of them belonged to previously annotated CDSs, and are therefore promising putative de novo genes, while most were located in intergenic regions and are thus newly discovered. Our results demonstrate the abundance of translation events outside of conserved CDSs, and their role as starting material for the emergence of novel genes in plants. Significance statementA central open question in genome evolution is how novel protein-coding genes arise from noncoding nucleotide DNA sequences and eventually contribute to the stable repertoires of "canonical" genes. Here, we focused specifically on the early stages of this important evolutionary process, whereby previously non-coding intergenic nucleotide sequences eventually acquire open reading frames carrying signatures of active translation. This phenomenon has been crucially under-studied so far, especially in plants. By combining ribosome profiling data and a careful genome comparison strategy among closely related Arabidopsis species, our results demonstrate the pervasive translation and de novo origin of a large number of small intergenic ORFs and illustrate their role as starting material for the emergence of novel genes in plants. Key-words: de novo genes, Arabidopsis, pervasive translation, intergenic ORFs, ribosome profiling

genomics↗

bioRxiv2025

Orthologs of an essential orphan gene vary in their capacities for function and subcellular localization in Drosophila melanogaster

Orphan genes evolve rapidly, raising questions about whether their functions remain conserved or diverge across species. To address this, we investigated goddard (gdrd), an orphan gene essential for spermatogenesis in Drosophila melanogaster. Within the Drosophila genus, Gdrd proteins retain a conserved core structure but display substantial variation in length and primary sequence. Here we perform cross-species gene-swap assays in D. melanogaster testes to examine how these lineage-specific changes affect Gdrd function. Strikingly, the highly divergent D. mojavensis ortholog fully rescues fertility in gdrd null flies, suggesting that ancestral Gdrd acted within a conserved spermatogenesis pathway. By contrast, several orthologs, including one from a more closely related species, cannot substitute for the melanogaster gene. Cytological analysis shows that all divergent Gdrd orthologs retain some ability to interact with axonemes and ring centrioles, consistent with the proteins structural conservation, but many non-complementing orthologs display weaker axonemal binding. Furthermore, all tested orthologs exhibit divergent localizations to organellar structures. Using computational analyses and molecular dynamics simulations, we identified intrinsic protein qualities that may account for several observations made in the gene swap assays. Rescuing orthologs bear motifs with shared physicochemical properties in their intrinsically disordered regions, while non-rescuing variants exhibit structural instabilities. Taken together, these findings show that while Gdrds ancestral structure and interactions are conserved, several orthologs have undergone lineage-specific evolutionary changes.

genetics↗

bioRxiv2025

Cryptocercus genomes expand knowledge of adaptations to xylophagy and termite sociality

Subsociality and wood-eating or xylophagy are understood as key drivers in the evolution of eusociality in Blattodea (cockroaches and termites), two features observed in the cockroach genus Cryptocercus, the sister group of all termites. We present and analyse two new high-quality genomes from this genus, C. punctulatus from North America and C. meridianus from Southeast Asia, to explore the evolutionary transitions to xylophagy and subsociality within Blattodea. Our analyses reveal evidence of relaxed selection in both Cryptocercus and termites, indicating that a reduction in effective population size may have occurred in their subsocial ancestors. These findings challenge the expected positive correlation between dN/dS ratios and social complexity, as Cryptocercus exhibits elevated dN/dS values that may exceed those of eusocial termites. Additionally, we identify positive selection on mitochondrial ribosomal proteins and components of the NADH dehydrogenase complex, suggesting significant evolutionary changes in energy production. Future studies incorporating additional genomic data from diverse blattodean species are essential to elucidate the molecular mechanisms driving transitions to xylophagy and eusociality.

evolutionary biology↗

bioRxiv2025

Convergent Evolutionary Traces of Genomic Innovations and Depletions in Socially Parasitic Ants

Parasitism, a common strategy across life, often involves genomic reduction. Socially parasitic "slavemaking" ants provide an excellent model to study the evolution of this lifestyle. Here, we compared the genomes of four closely related, independently evolved parasite-host pairs and their outgroups to identify convergent patterns. While genome size and gene numbers remain relatively stable, parasites show increased positive and relaxed selection, more putative de novo genes which have recently emerged from previously non-coding regions, and a significant loss of chemical receptors, particularly those associated with the evolution of sociality. Hosts, however, retain many duplicated genes. Gene co-expression networks associated with nest-defence in hosts are rather conserved, while the network structure of raiding parasites is much more variable and reflects the independent evolutionary origin of social parasitism. Our findings suggest that while hosts primarily rely on existing molecular mechanisms for defence, parasite genome evolution is characterised by extensive, convergent gene loss, innovation, and network rewiring.

evolutionary biology↗

bioRxiv2024

Ancestral aryl sulfatases in the alkaline phosphatase family allow for greater increases in catalytic efficiency than extant variants

Characterizing the dynamics and functional shifts during protein evolution is essential, both for understanding protein evolution and for rationalizing efficient strategies for e.g. enzymes with desired and effective functions. Most proteins organize in families, sets of divergent sequences which share a common ancestor and have a similar structural fold. We study aryl sulfatases (ASs), a subfamily of the large and evolutionary old alkaline phosphatase superfamily. In this manuscript we present how ultrahigh-throughput droplet micro-fluidics can be used for studying aryl sulfatases and their computationally reconstructed putative common ancestors. We compare the evolvability and robustness of three ancestors and four extant ASs which all exhibit catalytic promiscuity towards a range of substrate classes. Fourteen libraries with varying mutation rates were expressed in single-cell microdroplets. In general, higher mutation rates resulted in wider distribution of active variants but fewer improved variants overall. However, the impact of mutation rate differed between enzymes, with some benefiting from higher and others from lower mutation rate, underscoring the need to test diverse mutagenesis regimes.

evolutionary biology↗

bioRxiv2024

Reduced regulatory complexity associated with the evolutionary transition to sociality from cockroaches to termites despite evolutionary parallels with Hymenoptera

The degree of phenotypic diversity within social species has previously been associated with more complex genetic regulation both in cis and trans contexts. Transcription factors (TFs) being key to genetic regulation, have been studied in the origins of eusociality in Hymenoptera (bees, ants and wasps) but less so in Blattodea (cockroaches and termites). Here we show that the social transition in Blattodea, from cockroaches to termites, displays similar patterns of regulatory change to those found in Hymenoptera. Specifically, by analysing 3 cockroach and 5 termite genomes, we find more TF families with relaxed selection compared to intensified selection and lineage-specific gene family expansions in termites, which has also been reported in Hymenoptera. We also find that genes under selection support neotenic caste determination. We find there are key differences in Blattodea TF regulation in comparison with Hymenoptera with contractions in TF gene families and no compensatory change in TF DNA binding motifs either in frequency or diversity in TF promoter regions. Furthermore, we show that an increase in social complexity leads to greater diversity in TF activating domains, one of the evolutionary and structural building blocks of TFs, meanwhile, DNA-binding domains, undergo very little change. This study highlights similarities in social transitions between Hymenoptera and Blattodea, with evidence of large changes in transcriptional regulation followed by lineage specific adaptations. Our results indicate that the transcriptional diversity linked to social complexity is not attributable to transcription factors, but is instead likely driven by an alternative mechanism.. Significance statementIt has been widely reported that increased phenotypic complexity, particularly arising from social transitions, is often accompanied by increased regulatory complexity followed by lineage-specific adaptations. While extensively studied in Hymenoptera (bees, ants, and wasps), it has been less explored in Blattodea (cockroaches and termites). By examining the evolution of transcription factors across Blattodea, we investigated the regulatory changes associated with this social transition. Our study reveals that increased social complexity in Blattodea is accompanied by a reduction in regulatory complexity, including decreases in transcription factor numbers and no compensatory change in TF promoter binding site diversity or regulation. This study highlights that social transitions in Blattodea and Hymenoptera share a common pattern of large regulatory changes followed by lineage-specific adaptations.

evolutionary biology↗

bioRxiv2024

De novo ORFs are more likely to shrink than to elongate during neutral evolution.

For protein coding genes to emerge de novo from a non-genic DNA, the DNA sequence must gain an open reading frame (ORF) and the ability to be transcribed. The newborn de novo gene can further evolve to accumulate changes in its sequence. Consequently, it can also elongate or shrink with time. Existing literature shows that older de novo genes have longer ORF, but it is not clear if they elongated with time or remained of the same length since their inception. To address this question we developed mathematical model of ORF elongation as a Markov-jump process, and show that ORFs tend to keep their length in short evolutionary timescales. We also show that if change occurs it is likely to be a truncation. Our genomics and transcriptomics data analyses of seven Drosophila melanogaster populations is also in agreement with the models prediction. We conclude that selection could facilitate ORF length extension that may explain why longer ORFs were observed in old de novo genes in studies analysing longer evolutionary time scales. SignificanceNew protein coding genes can emerge from non-genic DNA through a process called de novo gene emergence. Genes thus emerged usually have a small open reading frame (ORF). However, studies show that de novo genes with an older evolutionary origin have longer ORF than younger genes. To understand how ORF length evolves, we use a combination of mathematical modeling and population level genome data analysis. We find that in the absence of evolutionary selection, ORFs tend to become shorter than becoming longer. Therefore, long ORFs are probably selected by evolution to be retained in the genome.

evolutionary biology↗

bioRxiv2024

High-throughput selection of human de novo-emerged sORFs with high folding potential

De novo genes emerge from previously non-coding stretches of the genome. Their en-coded de novo proteins are generally expected to be similar to random sequences and, accordingly, with no stable tertiary fold and high predicted disorder. However, structural properties of de novo proteins and whether they differ during the stages of emergence and fixation have not been studied in depth and rely heavily on predictions. Here we generated a library of short human putative de novo proteins of varying lengths and ages and sorted the candidates according to their structural compactness and disorder propensity. Using Forster resonance energy transfer (FRET) combined with Fluorescence-activated cell sorting (FACS) we were able to screen the library for most compact protein structures, as well as most elongated and flexible structures. Compact de novo proteins are on average slightly shorter and contain lower predicted disorder than less compact ones. The predicted structures for most and least compact de novo proteins correspond to expectations in that they contain more secondary structure content or higher disorder content, respectively. Our experiments indicate that older de novo proteins have higher compactness and structural propensity compared to young ones. We discuss possible evolutionary scenarios and their implications underlying the age-dependencies of compactness and structural content of putative de novo proteins.

evolutionary biology↗

bioRxiv2023

DNA Transposons favour de novo transcript emergence through enrichment of transcription factor binding motifs

De novo genes emerge from non-coding regions of genomes via succession of mutations. Among others, such mutations activate transcription and create a new open reading frame (ORF). Although the mechanisms underlying ORFs emergence are well documented, relatively little is known about the mechanisms enabling new transcription events. Yet, in many species a continuum between absent and very prominent transcription has been reported for essentially all regions of the genome. In this study we searched for de novo transcripts by using newly assembled genomes and transcriptomes of seven inbred lines of Drosophila melanogaster, originating from six European and one African population. This setup allowed us to detect line specific de novo transcripts, and compare them to their homologous non-transcribed regions in other lines, as well as genic and intergenic control sequences. We studied the association with transposable elements and the enrichment of transcription factor motifs upstream of de novo emerged transcripts and compared them with regulatory elements. We found that de novo transcripts overlap with TEs more often than expected by chance. The emergence of new transcripts correlates with high CpG islands and regions of TEs activity. Moreover, upstream regions of de novo transcripts are highly enriched with regulatory motifs. Such motifs abound in new transcripts overlapping with TEs, particularly DNA TEs, and are more conserved upstream de novo transcripts than upstream their non-transcribed homologs. Overall, our study demonstrates that TEs insertion is important for transcript emergence, partly by introducing new regulatory motifs from DNA TE families.

genomics↗

bioRxiv2023

How antisense transcripts can evolve to encode novel proteins

Protein coding features can emerge de novo in non coding transcripts, resulting in emer- gence of new protein coding genes. Studies across many species show that a large frac- tion large fraction of evolutionarily novel non-coding RNAs have an antisense overlap with protein coding genes. The open reading frames (ORFs) in these antisense RNAs could also overlap with existing ORFs. In this study, we investigate how the evolution an ORF could be constrained by its overlap with an existing ORF in three different read- ing frames. Using a combination of mathematical modeling and genome/transcriptome data analysis in two different model organisms, we show that antisense overlap can increase the likelihood of ORF emergence and reduce the likelihood of ORF loss, es- pecially in one of the three reading frames. In addition to rationalising the repeatedly reported prevalence of de novo emerged genes in antisense transcripts, our work also provides a generic modeling and an analytical framework that can be used to under- stand evolution of antisense genes.

evolutionary biology↗

bioRxiv2023

High turnover of de novo transcripts in Drosophila melanogaster

Most of the transcribed eukaryotic genomes are composed of non-coding transcripts. Among these transcripts, some are newly transcribed when compared to outgroups and are referred to as de novo transcripts. De novo transcripts have been shown to play a major role in de novo gene emergence. However, little is known about the rates at which de novo transcripts are gained and lost in individuals of the same species. Here, we address this gap and estimate for the first time the de novo transcript turnover rate. We use DNA long reads and RNA short reads from seven samples of inbred individuals of Drosophila melanogaster to detect de novo transcripts that are (transiently) gained on a short evolutionary time scale. Overall, each sampled individual contains between 2,320 and 2,809 unspliced de novo transcripts with most of them being sample specific. We estimate that around 0.15 transcripts are gained per year, and that each gained transcript is lost at a rate around 5x10-5 per year. This high turnover of transcripts suggests frequent exploration of new genomic sequences within species. These rates provide first empirical estimates to better predict and comprehend the process of de novo gene birth.

genomics↗

bioRxiv2023

Neutral models of de novo gene emergence suggest that gene evolution has a preferred trajectory

New protein coding genes can emerge from genomic regions that previously did not contain any genes, via a process called de novo gene emergence. To synthesize a protein, DNA must be transcribed as well as translated. Both processes need certain DNA sequence features. Stable transcription requires promoters and a polydenylation signal, while translation requires at least an open reading frame (ORF). We develop mathematical models based on mutation probabilities, and the assumption of neutral evolution, to find out how quickly genes emerge and are lost. We also investigate the effect of the order by which DNA features evolve, and if sequence composition is biased by mutation rate. We rationalize how genes are lost much more rapidly than they emerge, and how genes with long ORFs preferentially arise in regions that are already transcribed. Our study not only answers some fundamental questions on the topic of de novo emergence but also provides a modeling framework for future studies.

evolutionary biology↗

bioRxiv2023

Origin Matters: Using a Local Reference Genome Improves Measures in Population Genomics

Genome-level sequencing enables us to ask fundamental questions about the genetic basis of adaptation, population structure, and epigenetic mechanisms, but usually requires a suitable reference genome for mapping population-level re-sequencing data. In some model systems, multiple reference genomes are available, giving researchers the challenging task of determining which reference genome best suits their data. Here we compare the use of two different reference genomes for the three-spined stickleback (Gasterosteus aculeatus), one novel genome derived from a European gynogenetic individual and the published reference genome of a North American individual. Specifically, we investigate the impact of using a local reference versus one generated from a distinct lineage on several common population genomics analyses. Through mapping genome resequencing data of 60 sticklebacks from across Europe and North America, we demonstrate that genetic distance among samples and the reference impacts downstream analyses. Using a local reference genome increased mapping efficiency and genotyping accuracy, effectively retaining more and better data. Despite comparable distributions of the metrics generated across the genome using SNP data (i.e., {pi}, Tajimas D, and FST), window-based statistics using different references resulted in different outlier genes and enriched gene functions. A marker-based analysis of DNA methylation distributions had a comparably high overlap in outlier genes and functions, yet with distinct differences depending on the reference genome. Overall, our results highlight how using a local reference genome decreases reference bias to increase confidence in downstream analyses of the data. Such results have significant implications in all reference-genome-based population genomic analyses.

bioinformatics↗

bioRxiv2022

Population genomics reveals mechanisms and dynamics of de novo proto-gene emergence in Drosophila melanogaster

Scientific AbstractNovel genes are essential for evolutionary innovations and differ substantially even between closely related species. Recently, multiple studies across many taxa have suggested that some novel genes arise de novo, i.e. from previously non-coding DNA. In order to characterise the underlying mutations that allowed de novo gene emergence and their order of occurrence, homologous regions must be detected within non-coding sequences in closely related sister genomes. So far, most studies do not detect non-coding homologs of de novo genes due to inconsistent data and long evolutionary distances separating genomes. Here we overcome these issues by searching for proto-genes, the not-yet fixed precursors of de novo genes that emerged within a single species. We sequenced and assembled genomes with long-read technology and the corresponding transcriptomes from inbred lines of Drosophila melanogaster, derived from seven geographically diverse populations. We found line-specific proto-genes in abundance but few proto-genes shared by lines, suggesting a rapid turnover. Gain and loss of transcription is more frequent than the creation of Open Reading Frames (ORFs), e.g. by forming new START- and STOP-codons. Consequently, the gain of ORFs becomes rate limiting and is frequently the initial step in proto-gene emergence. Furthermore, Transposable Elements (TEs) are major drivers for intra genomic duplications of proto-genes, yet TE insertions are less important for the emergence of proto-genes. However, highly mutable genomic regions around TEs provide new features that enable gene birth. In conclusion, proto-genes have a high birth-death rate, are rapidly purged, but surviving proto-genes spread neutrally through populations and within genomes.

genomics↗

bioRxiv2022

Chaperones facilitate heterologous expression of naturally evolved putative de novo proteins

Over the past decade, evidence has accumulated that new protein coding genes can emerge de novo from previously non-coding DNA. Most studies have focused on large scale computational predictions of de novo protein coding genes across a wide range of organisms. In contrast, experimental data concerning the folding and function of de novo proteins is scarce. This might be due to difficulties in handling de novo proteins in vitro, as most are predicted to be short and disordered. Here we propose a guideline for the effective expression of eukaryotic de novo proteins in Escherichia coli. We used 11 sequences from Drosophila melanogaster and 10 from Homo sapiens, that are predicted de novo proteins from former studies, for heterologous expression. The candidate de novo proteins have varying secondary structure and disorder content. Using multiple combinations of purification tags, E. coli expression strains and chaperone systems, we were able to increase the number of solubly expressed putative de novo proteins from 30 % to 62 %. Our findings indicate that the best combination for expressing putative de novo proteins in E.coli is a GST-tag with T7 Express cells and co-expressed chaperones. We found that, overall, proteins with higher predicted disorder were easier to express.

molecular biology↗

bioRxiv2022

Live-bearing cockroach genome reveals convergent evolutionary mechanisms linked to viviparity in insects and beyond

Insects provide an unparalleled opportunity to link genomic changes with the rise of novel phenotypes, given tremendous variation in the numerous and complex adaptations displayed across the group. Among these numerous and complex adaptations, live-birth has arisen repeatedly and independently in insects and across the tree of life, suggesting this is one of the most common types of convergent evolution among animals. We sequenced the genome and transcriptome of the Pacific beetle-mimic cockroach, the only truly viviparous cockroach, and performed comparative analyses including two other viviparous insect lineages, the tsetse and aphids, to unravel the genomic basis underlying the transition to viviparity in insects. We identified pathways experiencing adaptive evolution, common in all viviparous insects surveyed, involved in uro-genital remodeling, maternal control of embryo development, tracheal system, and heart development. Our findings suggest the essential role of those pathways for the development of placenta-like structure enabling embryo development and nutrition. Viviparous transition seems also to be accompanied by the duplication of genes involved in eggshell formation. Our findings from the viviparous cockroach and tsetse reveal that genes involved in uterine remodeling are up-regulated and immune genes are down-regulated during the course of pregnancy. These changes may facilitate structural changes to accommodate developing young and protect them from the mothers immune system. Our results denote a convergent evolution of live-bearing in insects and suggest similar adaptive mechanisms occurred in vertebrates, targeting pathways involved in eggshell formation, uro-genital remodeling, enhanced tracheal and heart development, and reduced immunity.

genomics↗