Strength in numbers: collaborative science for new experimental model systems

Waller, Ross F.; Cleves, Phillip A.; Rubio-Brotons, Maria; Woods, April; Bender, Sara J.; Edgcomb, Virginia P.; Gann, Eric R.; Jones, Adam C.; Teytelman, Leonid; Dassow, Peter von; Wilhelm, Steven W.; Collier, Jackie

doi:10.1101/308304

Cited by 5 publications

(5 citation statements)

References 15 publications

(14 reference statements)

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“…In all these organisms, multispectral fluorescence imaging showed that multiple TUs are successfully expressed from uLoop plasmids. Special attention was devoted to testing uLoop in P. tricornutum, recognising the special needs for genetic tools in such emerging model organisms and the need for new marine microbial model systems (39). The uLoop plasmids were efficiently introduced in P. tricornutum, in which exconjugants exhibited variable levels of fluorescent protein expression.…”

Section: Use Of Uloop Vectors Across Biological Kingdomsmentioning

confidence: 99%

Universal Loop assembly (uLoop): open, efficient, and species-agnostic DNA fabrication

Pollak

Matute

Núñez

et al. 2019

Preprint

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Standardised Type IIS DNA assembly methods are becoming essential for biological engineering and research. Although a 'common syntax' has been proposed to enable higher interoperability between DNA libraries, Golden Gate (GG) -based assembly systems remain specific to target organisms. Furthermore, these GG assembly systems become laborious and unnecessarily complicated beyond the assembly of 4 transcriptional units. Here, we describe "universal Loop" (uLoop) assembly, a simple system based on Loop assembly that enables hierarchical fabrication of large DNA constructs (> 30 kb) for any organism of choice. uLoop comprises two sets of four plasmids that are iteratively used as odd and even levels to compile DNA elements in an exponential manner (4 n-1 ). The elements required for transformation/maintenance in target organisms are also assembled as standardised parts, enabling customisation of host-specific plasmids. Thus, this species-agnostic method decouples efficiency of assembly from the stability of vectors in the target organism. As a proof-of-concept, we show the engineering of multi-gene expression vectors in diatoms, yeast, plants and bacteria. These resources will become available through the OpenMTA for unrestricted sharing and open-access. !

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Section: Use Of Uloop Vectors Across Biological Kingdomsmentioning

confidence: 99%

Universal Loop assembly (uLoop): open, efficient, and species-agnostic DNA fabrication

Pollak

Matute

Núñez

et al. 2019

Preprint

Self Cite

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“…The phosphorylation dataset spans the Tree of Life but is unsurprisingly biased towards animal, fungal, and plant species. Ongoing projects for increased representation of the protist superkingdoms could help to address this problem in the future (Waller et al 2018). From this analysis also we conclude that most eukaryotic phosphomotifs post-date the divergence of eukaryotes and prokaryotes.…”

Section: Discussionmentioning

confidence: 66%

Evolution of protein kinase substrate recognition at the active site

Bradley

Beltrão

2018

Preprint

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Protein kinases catalyse the phosphorylation of target proteins, controlling most cellular processes. The specificity of serine/threonine kinases is partly determined by interactions with a few residues near the phospho-acceptor residue, forming the socalled kinase substrate motif. Kinases have been extensively duplicated throughout evolution but little is known about when in time new target motifs have arisen. Here we show that sequence variation occurring early in the evolution of kinases is dominated by changes in specificity determining residues. We then analysed kinase specificity models, based on known target sites, observing that specificity has remained mostly unchanged for recent kinase duplications. Finally, analysis of phosphorylation data from a taxonomically broad set of 48 eukaryotic species indicates that most phosphorylation motifs are broadly distributed in eukaryotes but not present in prokaryotes. Overall, our results suggest that the set of eukaryotes kinase motifs present today was acquired soon after the eukaryotic last common ancestor and that early expansions of the protein kinase fold rapidly explored the space of possible target motifs.

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“…This transformation will be unlocked by coupling genomic data with current high-throughput approaches such as in vitro TF sequence binding affinity assays, genome-wide profiling of TF binding, and proteomics studies of chromatin beyond model species [50]. Additionally, the establishment of genetic manipulation tools in species representing unsampled eukaryotic lineages will crucially open the window to both targeted studies and genetic screens [51,52]. The comparative analysis and interpretation of these data will ultimately allow us to uncover general principles of TF regulation across eukaryotes and it will contribute to reconstruct the cellular and regulatory biology of the LECA.…”

Section: Discussionmentioning

confidence: 99%

Origin and evolution of eukaryotic transcription factors

Mendoza

Sebé-Pedrós

2019

Current Opinion in Genetics & Development

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Transcription factors (TFs) have a central role in genome regulation directing gene transcription through binding specific DNA sequences. Eukaryotic genomes encode a large diversity of TF classes, each defined by unique DNA-interaction domains. Recent advances in genome sequencing and phylogenetic placement of diverse eukaryotic and archaeal species are redefining the evolutionary history of eukaryotic TFs. The emerging view from a comparative genomics perspective is that the Last Eukaryotic Common Ancestor (LECA) had an extensive repertoire of TFs, most of which represent eukaryotic evolutionary novelties. This burst of TF innovation coincides with the emergence of genomic nuclear segregation and complex chromatin organization.pronounced in plants and animals, both of which encode the most diverse and abundant TF repertoires [3]. This review discusses the emergence and diversification of eukaryotic TF classes, as well as the modes of TF acquisition and the evidence of conserved TF functionality across eukaryotes. Revisiting Transcription Factor diversity across the tree of lifeThe continuously growing availability of genome sequence data from key branches of the tree of life is transforming our understanding of the evolution of major eukaryotic gene families. For example, several deep-branching eukaryotic species have recently been either described and/or sequenced for the first time [5][6][7][8]. Similarly, the discovery and placement of Asgard archaea as the sister group to eukaryotes reshaped our view on eukaryotic origins [9,10]. Although there is not yet a consensus on the phylogenetic root of eukaryotes, phylogenomic analyses have reduced the potential eukaryotic tree topologies to a few alternative options, which chiefly differ on the phylogenetic position of Discoba and Metamonada [5,11]. Taking advantage of these new genomic data, we reviewed the distribution of a curated list of DBDs representing 74 TF classes in 158 eukaryotic species, 265 archaea and 5,394 bacteria (Figure 1, 2) [12]. Some TF classes have pre-eukaryotic origins. For example, the basal transcription factor machinery is present in multiple archaeal species [13,14], including the TBP (TATA box binding protein), NFYB (Nuclear transcription factor Y subunit beta) and the TFIIB (Figure 2). CSD TFs are also found across all domains of life. Interestingly, some Asgard archaea also encode E2F/TDP, which is a key cell cycle regulator in eukaryotes [15]. This constitutes a new example of a gene family shared between Asgard archaea and eukaryotes but absent from other archeal lineages [9,10], thus reinforcing the view of an Asgard-like ancestor as the initial step towards eukaryogenesis. An additional group of TFs are found in a small number of bacterial species. For example, AP2 and Myb TFs are found in 149 and 257 bacterial species respectively. There are three possible explanations for these observed distributions. First, this could indicate that these TFs have bacterial origins [13]. Second, some bacterial lineages could have acquired eukary...

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Strength in numbers: collaborative science for new experimental model systems

Cited by 5 publications

References 15 publications

Universal Loop assembly (uLoop): open, efficient, and species-agnostic DNA fabrication

Universal Loop assembly (uLoop): open, efficient, and species-agnostic DNA fabrication

Evolution of protein kinase substrate recognition at the active site

Origin and evolution of eukaryotic transcription factors

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