Vector redesign and in-droplet cell-growth improves enrichment and recovery in live Escherichia coli
In this article we compare different methods to sort large libraries of enzymes presented on the surface of E. coli, and recovering the intact cells without lysis. We changed a protocol in which single cells encapsulated in a microdroplet are measured using Fluorescence-activated droplet sorting (FADS) to a protocol were cells are grown inside a microdroplet after encapsulation of a single cell, resulting in multiple copies of the same variant inside each droplet. We find that growing cells inside a microdroplet prior to FADS increases both the amount of cells recovered as well as reducing the amount of false positives.
The role of transposable elemets in the evolution of insect socal complexity - Erich Bornberg-Bauer at the HFSP meeting in Paris
This time the group leader Erich Bornberg-Bauer himself presented our work on the role of transposable elements in termites. The 21st HFSP Awardees meeting took place in beautiful Paris this year. The poster is based on work by postdoc Mark Harrison and former postdoc Evelien Jongepier from our group in cooperation with Mireille Vasseur-Cognet (Paris), Hei Sook Sul (Berkeley) and Wilhelm de Beer (Pretoria).
We compared whole-genome levels of repeat element transcription in the fat body of female workers, kings, and five different queen stages. Those queens can live over 20 years, maintaining near maximum reproductive output! The sterile workers only live weeks or months. We found substantially higher TE activity in workers than in reproductives. Furthermore, relative TE expression decreased with age in queens, due to a significant upregulation of the PIWI-pathway in 20-year-old queens. Our results suggest a caste- and age-specific regulation of the PIWI-pathway has evolved in higher termites that is analogous to germ-line-specific activity in individual organisms, promoting reproductive fitness even at high age.
Evidence for a conserved queen-worker genetic toolkit across slave-making ants and their ant hosts
The ecological success of social Hymenoptera (ants, bees, wasps) depends on the division of labour between the queen and workers. Each caste exhibits highly specialized morphology, behaviour, and life-history traits, such as lifespan and fecundity. Despite strong defences against alien intruders, insect societies are vulnerable to social parasites, such as workerless inquilines or slave-making ants. Here, we investigate whether gene expression varies in parallel ways between lifestyles (slave-making versus host ants) across five independent origins of ant slavery in the “Formicoxenus-group” of the ant tribe Crematogastrini. As caste differences are often less pronounced in slave-making ants than in nonparasitic ants, we also compare caste-specific gene expression patterns between lifestyles. We demonstrate a substantial overlap in expression differences between queens and workers across taxa, irrespective of lifestyle. Caste affects the transcriptomes much more profoundly than lifestyle, as indicated by 37 times more genes being linked to caste than to lifestyle and by multiple caste-associated modules of coexpressed genes with strong connectivity. However, several genes and one gene module are linked to slave-making across the independent origins of this parasitic lifestyle, pointing to some evolutionary convergence. Finally, we do not find evidence for an interaction between caste and lifestyle, indicating that caste differences in gene expression remain consistent even when species switch to a parasitic lifestyle. Our findings strongly support the existence of a core set of genes whose expression is linked to the queen and worker caste in this ant taxon, as proposed by the “genetic toolkit” hypothesis.
Anna Grandchamp and Alina Mikhailova present their work at ESEB in Prague
MC Harrison on ICE (International Congress of Entomology)
Complex regulatory role of DNA methylation in caste- and age-specific expression of a termite
The reproductive castes of eusocial insects are often characterized by extreme lifespans and reproductive output, indicating an absence of the fecundity/ longevity trade-off. The role of DNA methylation in the regulation of caste- and age-specific gene expression in eusocial insects is controversial. While some studies find a clear link to caste formation in honeybees and ants, others find no correlation when replication is increased across independent colonies. Although recent studies have identified transcription patterns involved in the maintenance of high reproduction throughout the long lives of queens, the role of DNA methylation in the regulation of these genes is unknown. We carried out a comparative analysis of DNA methylation in the regulation of caste-specific transcription and its importance for the regulation of fertility and longevity in queens of the higher termite Macrotermes natalensis. We found evidence for significant, well-regulated changes in DNA methyl- ation in mature compared to young queens, especially in several genes related to ageing and fecundity in mature queens. We also found a strong link between methylation and caste-specific alternative splicing. This study reveals a complex regulatory role of fat body DNA methylation both in the div- ision of labour in termites, and during the reproductive maturation of queens.
Heterologous expression of naturally evolved putative de novo proteins with chaperones
Today, we know that proteins do not only evolve by duplication and divergence of existing proteins but also arise from previously non-coding DNA. These proteins are called de novo proteins. Their properties are still poorly understood and their experimental analysis faces major obstacles. Here, we aim to present a starting point for soluble expression of de novo proteins with the help of chaperones and thereby enable further characterization.
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 are scarce. This might be due to difficulties in handling de novo proteins in vitro, as most are short and predicted to be 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 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%. We found that, overall, proteins with higher predicted disorder were easier to express.
Janina (GadauLab) and Lars elected as IEB student representatives
Our PhD student Lars and Janina Rinke from the lab of Jürgen Gadau were elected as IEB student representatives for the next two years!
Master Defence Christopher Finke: "Genome annotation and comparison of genomic features between slave-maker ants and their hosts"
Our dear student Christopher Finke has successfully defended his Master thesis yesterday evening. Supervised by Alice Séguret he looked into differences between slave-maker ants and their host species and was able to generate valuable genome annotations. Christopher started out as a Bachelor student in the lab with us and moved on to computational work during his Master studies. Congratulations and good luck in Berlin!
Plant biodiversity assessment through soil eDNA reflects temporal and local diversity
The use of environmental DNA as a proxy to identify species has increased exponentially in the last few years. However, how good eDNA relates with actual species presence/abundance remains elusive. Our study fill this gap, comparing both soil eDNA and visual assessments of plants in Norway. It shows that soil eDNA allows to describe well local plant biodiversity, with an average 60% match with visual survey for vascular plants, and also to recover past vegetation biodiversity. Our soil eDNA method then provide a great tool to assess rapidly plant biodiversity in any seasons.
PhD students Margaux and Lars presenting their posters at Apfed22 in Bayreuth
Our PhD students Margaux Aubel and Lars Eicholt presented their most recent work on soluble expression of putative de novo proteins at Apfed22 in Bayreuth! If you did not attend, please check out their preprints here and here. We would like to thank all the organizers for this amazing hybrid conference. The speaker line-up was diverse both in backgrounds and research areas, while reaching gender parity!
Co-expression analyses, combined with lipidomics and metabolomics, uncover lifespan prolonging mechanisms in extremely long-lived and highly fertile termite queens
Sarah Séité, Mark C Harrison, David Sillam-Dussès, Roland Lupoli, Tom J M Van Dooren, Alain Robert, Laure-Anne Poissonnier, Arnaud Lemainque, David Renault, Sébastien Acket, Muriel Andrieu, José Viscarra, Hei Sook Sul, Z Wilhelm de Beer, Erich Bornberg-Bauer , Mireille Vasseur-Cognet Communications Biology
Some insects are eusocial, which means that their society is organized into different castes which carry out specific colony tasks. In termites, for example, the “king” and the “queen” are involved in reproduction, while the “workers” are involved in resource gathering and brood-care. Macrotermes natalensis is a species of higher termite that creates large complex colonies, in which the king and the queen (reproductives) have a long life, spanning decades, and the queen remains highly fertile throughout her adult life. Workers, on the other hand, are short-lived and sterile. We studied this species of termites, using a combination of high throughput techniques such as transcriptomics, metabolomics and lipidomics, to identify mechanisms that allow reproductives to live orders of magnitude longer than workers, while maintaining high fertility. Aging associated genes were differentially expressed between the reproductives and the workers. For example, antioxidant genes were highly expressed, and the membrane lipids were less damaged by oxidative stress, in the queens relative to workers. Contrary to expectations, we found that several members of the insulin/insulin-like growth factor signaling (IIS) pathway were upregulated in the queens. Normally this would indicate increased diversion of metabolism towards energy storage. However, we did not find excessive fat storage in the queens; simple sugars dominate in their hemolymph and a large amount of resources is allocated to egg production. Our findings support the notion that aging results from a complex interplay of several processes. These processes should be studied simultaneously and not in isolation, for a better understanding of aging.
Convergent loss of chemoreceptors across independent origins of slave-making in ants
Socially parasitic ants exploit the work force and social organisation of closely related ant species, and therefore no longer need to perform certain social tasks such as brood care and foraging. The loss of such behaviours is expected to be accompanied by loss of the underlying genes. We sequenced the genomes of eight ant species representing three independent origins of parasitism. Due to their importance in chemical communication and foraging, we investigated the evolution of chemoreceptors in parasites and their hosts. We found that parasites lost a striking 50% of their gustatory receptor repertoire compared to their hosts, perhaps reflecting the outsourcing of foraging tasks to host workers. We also found that parasites had fewer olfactory receptors than their hosts, with the same olfactory receptors being lost across multiple origins of parasitism. This represents a rare case of convergent molecular evolution at the level of individual genes, shedding light on the loss of important social traits during the transition to a parasitic lifestyle.
Ancestral sequences of a large promiscuous enzyme family correspond to bridges in sequence space in a network representation
Evolutionary relationships of protein families can be characterized either by networks or by trees. Whereas trees allow for hierarchical grouping and reconstruction of the most likely ancestral sequences, networks lack a time axis but allow for thresholds of pairwise sequence identity to be chosen and, therefore, the clustering of family members with presumably more similar functions. Here, we use the large family of arylsulfatases and phosphonate monoester hydrolases to investigate similarities, strengths and weaknesses in tree and network representations. For varying thresholds of pairwise sequence identity, values of betweenness centrality and clustering coefficients were derived for nodes of the reconstructed ancestors to measure the propensity to act as a bridge in a network. Based on these properties, ancestral protein sequences emerge as bridges in protein sequence networks. Interestingly, many ancestral protein sequences appear close to extant sequences. Therefore, reconstructed ancestor sequences might also be interpreted as yet-to-be-identified homologues. The concept of ancestor reconstruction is compared to consensus sequences, too. It was found that hub sequences in a network, e.g. reconstructed ancestral sequences that are connected to many neighbouring sequences, share closer similarity with derived consensus sequences. Therefore, some reconstructed ancestor sequences can also be interpreted as consensus sequences.
New research priorities in Münster
Die Deutsche Forschungsgemeinschaft (DFG) fördert zwei neue Schwerpunktprogramme (SSP) an der Westfälischen Wilhelms-Universität in Münster. Insgesamt fließen dafür in den nächsten drei Jahren 10 bis 14 Millionen Euro nach Münster. Gefördert werden Programme in der Biologie und der Chemie. Im Projekt „Die genomischen Grundlagen evolutionärer Innovationen (GEvol)“ unter der Leitung des Biologen Prof. Dr. Erich Bornberg-Bauer vom Institut für Evolution und Biodiversität wollen die Forscher die Mechanismen der genetischen Veränderungen einer großen Artengruppe entschlüsseln. „In dem Vorhaben untersuchen wir unter anderem die Prozesse, die den wichtigsten genomischen Veränderungen in der Evolution zugrunde liegen – beispielsweise Gewinn und Verlust von Sozialität oder Paarungssystemen, Verteidigung und Immunität, entwicklungsbiologischen und morphologischen Anpassungen“, sagt Erich Bornberg-Bauer. Read more
Münster University receives two new research associations
The University of Münster is coordinating two new Priority Programmes funded by the German Research Foundation (DFG) with several million euros. The projects come from the fields of biology and chemistry and deal with innovative informatics technologies.Read more
Structural and functional characterization of a putative de novo gene in Drosophila
Comparative genomic studies have repeatedly shown that new protein-coding genes can emerge de novo from noncoding DNA. Still unknown is how and when the structures of encoded de novo proteins emerge and evolve. Combining biochemical, genetic and evolutionary analyses, we elucidate the function and structure of goddard, a gene which appears to have evolved de novo at least 50 million years ago within the Drosophila genus. Previous studies found that goddard is required for male fertility. Here, we show that Goddard protein localizes to elongating sperm axonemes and that in its absence, elongated spermatids fail to undergo individualization. Combining modelling, NMR and circular dichroism (CD) data, we show that Goddard protein contains a large central α-helix, but is otherwise partially disordered. We find similar results for Goddard’s orthologs from divergent fly species and their reconstructed ancestral sequences. Accordingly, Goddard’s structure appears to have been maintained with only minor changes over millions of years.
New proteins 'out of nothing'
Proteins are the key component in all modern forms of life. Haemoglobin, for example, transports the oxygen in our blood; photosynthesis proteins in the leaves of plants convert sunlight into energy; and fungal enzymes help us to brew beer and bake bread. Researchers have long been examining the question of how proteins mutate or come into existence in the course of millennia. That completely new proteins - and, with them, new properties - can emerge practically out of nothing, was inconceivable for decades, in line with what the Greek philosopher Parmenides said: "Nothing can emerge from nothing" (ex nihilo nihil fit). Working with colleagues from the USA and Australia, researchers from the University of Münster (Germany) have now reconstructed how evolution forms the structure and function of a newly emerged protein in flies. This protein is essential for male fertility. The results have been published in the journal "Nature Communications". Read more
Marie Skłodowska-Curie Actions | Individual Fellowship awarded to Dr. Bertrand Fouks
How genomes evolve and drive novelty is a central question in biology. Some of the most puzzling genomic innovations, for example the development of placenta in mammals, are triggered by Transposable Elements (TEs). TEs are small genome fragments that can move and insert in other areas of the genome, which can create or impair gene functions. Organisms have adapted mechanisms to counteract the harmful effects of TEs, notably small RNAs (e.g. piwi-interacting RNA, piRNAs). Despite increasing knowledge on the effects of TEs on genome evolution and the apparition of novel traits, how and which TEs along with their interactions with piRNAs can promote novelty remain unclear. The project of Dr. Fouks will shed light on this issue by investigating how TEs and piRNAs evolved and interacted in cockroaches and termites alongside the evolution of their incredible biodiversity, with an emphasis on sociality and wood feeding. Dr. Fouks will generate several high-resolution genomes and transcriptomes from cockroach and termite species to locate and categorize TEs and piRNAs., This will allow him to unravel their role in the adaptation of cockroaches and termites to different social levels and diets.
Humboldt Fellowship for Dr. Anna Grandchamp
Since several years it is known that new proteins not only arise via gene duplication and variation of the duplicates but also de novo, i.e. from previously non-coding DNA. An important first step in the creation of these de novo genes is that some of the zillions of randomly generated transcripts have some, though very weak, inherent function or are at least not toxic to the cell and are not quickly lost again. In her project, Dr. Grandchamp will investigate how often new random transcripts are created, by which mechanisms they are created and what the initial function of the new proteins might be.She plans to use in-bred lines of fly populations collected from all over Europe as well as of closely related fly species and map their transcriptomes onto the newly sequenced genomes to precisely characterise the creation and loss of de novo genes.
Researchers gain new insights into the evolution of proteins
How do bacteria manage to adapt to synthetic environmental toxins and to even develop strategies for using a pesticide agent as food within less than 70 years? This is what scientists at Münster University have investigated. They found out how mutations led to biochemical changes that now enable an enzyme to cleave a pesticide. The study was published in "Nature Chemical Biology". Read more
Bioinformaticians examine new genes the moment they are born
Accumulating evidence suggests that new genes can arise spontaneously from previously non-coding DNA instead of through the gradual mutation of established genes. Bioinformaticians at the University of Münster are now, for the first time, studying the earliest stages in the emergence of such “genes out of thin air”, also known as de novo genes. Read more
"The Elusive Calculus of Insect Altruism
In 1964, the evolutionary biologist William D. Hamilton seemingly explained one of the greatest paradoxes in biology with a simple mathematical equation. Even Charles Darwin had called the problem his “one special difficulty” a century earlier in On the Origin of Species, writing that it made him doubt his own theory. The paradox in question is the altruistic behavior exhibited most famously by social insects. Ants, termites, and some bees and wasps live in highly organized colonies in which most individuals are sterile or forgo reproduction, instead serving the select few who do lay eggs. Yet such behavior seemed to clearly violate the concept of natural selection and survival of the fittest, if “fittest” means the individual with the greatest reproductive success. The insects’ compulsory altruism—a form of extreme social behavior called eusociality—made little sense. Read more
"Human Frontier Science Program" funds two projects involving Münster University researchers
In the selection phase for 2018, the prestigious “Program Grant” research award given by the international “Human Frontier Science Program” goes to two members of the Department of Biology at the University of Münster – to bioinformatics specialist Prof. Erich Bornberg-Bauer and cell biologist Prof. Karin Busch. Read more
Consider the Cockroach
On the fringes of urban life, some creatures thrive more than others. The brown rat, the coyote, the Canada goose, the Northern raccoon and many other species have all expanded their ranges and populations because they are well-adapted to scavenge or hunt in the shadows of human civilization. But perhaps none have been as successful as the cockroach. Read more
The social evolution of termites
One phenomenon that already fascinated Charles Darwin is the evolution of huge, complex insect societies from solitary ancestors. This was the case with termites and ants, which have the same eusocial lifestyle. This has distinctive features such as the creation of castes, including for instance a complex system of division of labor among workers and soldiers. A team headed by evolutionary biologist Prof. Dr. Judith Korb from the University of Freiburg, bioinformatician Prof. Dr. Erich Bornberg-Bauer, evolutionary biologist Dr. Mark Harrison and evolutionary biologist Dr. Evelien Jongepier from the Westphalian Wilhelms University in Münster has now compared the molecular basis for the evolution of the eusocial lifestyle. Read more
Scientists investigate the molecular basis of social evolution in Termites
Researchers from the group of bioinformatician Prof Erich Bornberg-Bauer from the Institute for Evolution and Biodiversity at the WWU have now, for the first time, compared the molecular basis for the evolution of eusociality within termites and ants. Read more
Land plant became key marine species
The genome of eelgrass (Zostera marina) has now been unveiled. It turns out that the plant, once land-living but now only found in the marine environment, has lost the genes required to survive out of the water. Scientists from the University of Gothenburg participated in the research study, the results of which are published in the scientific journal Nature. Eelgrass belongs to a group of flowering plants that have adapted to a life in water. As such, it is a suitable candidate for studies of adaptation and evolution. 'Since flowering plants have emerged and developed on land, eelgrass can be expected to share many genetic features with many land plants. Studying differences between them can tell us how eelgrass has adapted to a marine environment,' says Mats Töpel, researcher at the Department of Marine Sciences, University of Gothenburg, who participated in the sequencing of the eelgrass genome. Töpel is part of an international research collaboration involving 35 research teams. As a result of their efforts, the eelgrass genome has now been published in Nature. Read more
A Surprise Source of Life's Code
Genes, like people, have families — lineages that stretch back through time, all the way to a founding member. That ancestor multiplied and spread, morphing a bit with each new iteration. For most of the last 40 years, scientists thought that this was the primary way new genes were born — they simply arose from copie s of existing genes. The old version went on doing its job, and the new copy became free to evolve novel functions. Read more
Tracking colony-building insects
Scientists have long been doing research into how the complicated system of living together in insect colonies functions. An international group of researchers – including scientists from Münster University – have now sequenced and analysed the genome of one type of termite. This means that they have now been able to compare the termites' DNA with that of ants and colony-building bees. The study has been published in "Nature Communications". Read more
Prestigious award for bioinformatician
Prof. Erich Bornberg-Bauer from the Institute for Evolution and Biodiversity at Münster University has received a prestigious Program Grant from the international "Human Frontier Science Program" (HFSP). With this grant the HFSP supports outstanding scientists from various countries who jointly work on innovative research topics. Read more
Enigma of Twisted-Wing Parasites resolved
Scientists have long been mystified by the insect group called twisted-wing parasite. It includes over 500 species and although it has been known for almost 200 years, till now it could not be linked to any super-ordinate group of insects. A team of scientists have, for the first time ever, sequenced the entire genetic code – the genome – of a twisted-wing parasite, thus enabling the scientists to classify these insects as a sister group of the beetle. Read more
Secrets of fungus-growing
An international consortium of researchers, including Prof. Erich Bornberg-Bauer from Münster University's Institute of Evolution and Biodiversity, has been able top demonstrate for the first time that the highly specialized lifestyle of leafcutter ants has been deposited in the insects' genetic make-up. For example, they are missing certain genes which are otherwise necessary for digestion. Read more
Bacteria change sperm of insects
Es ist ein recht gerissener Trick im Naturreich: Ein Bakterium sorgt dafür, dass sich sein Wirt erfolgreich vermehrt, indem er das Erbgut der Spermien verändert. Darin hatten Forscher überraschenderweise Teile des Bakterien-Genoms gefunden. Mit einem raffinierten genetischen Trick sichert das Bakterium Wolbachia sein Überleben in Insekten: Der Parasit manipuliert die Fortpflanzung seiner Wirte in großem Stil. Auf die Schliche gekommen ist dem Bakterium eine internationale Forschergruppe, die das Erbgut von Erzwespen entziffert und darin ein Gen des Schmarotzers entdeckt hat. Read more