Evolution of the holozoan ribosome biogenesis regulon

<p>Abstract</p> <p>Background</p> <p>The ribosome biogenesis (RiBi) genes encode a highly-conserved eukaryotic set of nucleolar proteins involved in rRNA transcription, assembly, processing, and export from the nucleus. While the mode of regulation of this suite of genes has been studied in the yeast, <it>Saccharomyces cerevisiae</it>, how this gene set is coordinately regulated in the larger and more complex metazoan genomes is not understood.</p> <p>Results</p> <p>Here we present genome-wide analyses indicating that a distinct mode of RiBi regulation co-evolved with the E(CG)-binding, Myc:Max bHLH heterodimer complex in a stem-holozoan, the ancestor of both Metazoa and Choanoflagellata, the protozoan group most closely related to animals. These results show that this mode of regulation, characterized by an E(CG)-bearing core-promoter, is specific to almost all of the known genes involved in ribosome biogenesis in these genomes. Interestingly, this holozoan RiBi promoter signature is absent in nematode genomes, which have not only secondarily lost Myc but are marked by invariant cell lineages typically producing small body plans of 1000 somatic cells. Furthermore, a detailed analysis of 10 fungal genomes shows that this holozoan signature in RiBi genes is not found in hemiascomycete fungi, which evolved their own unique regulatory signature for the RiBi regulon.</p> <p>Conclusion</p> <p>These results indicate that a Myc regulon, which is activated in proliferating cells during normal development as well as during tumor progression, has primordial roots in the evolution of an inducible growth regime in a protozoan ancestor of animals. Furthermore, by comparing divergent bHLH repertoires, we conclude that regulation by Myc but not by other bHLH genes is responsible for the evolutionary maintenance of E(CG) sites across the RiBi suite of genes.</p

Temporal Regulation of the Muscle Gene Cascade by Macho1 and Tbx6 Transcription Factors in Ciona Intestinalis

For over a century, muscle formation in the ascidian embryo has been representative of \u27mosaic\u27 development. The molecular basis of muscle-fate predetermination has been partly elucidated with the discovery of Macho1, a maternal zinc-finger transcription factor necessary and sufficient for primary muscle development, and of its transcriptional intermediaries Tbx6b and Tbx6c. However, the molecular mechanisms by which the maternal information is decoded by cis-regulatory modules (CRMs) associated with muscle transcription factor and structural genes, and the ways by which a seamless transition from maternal to zygotic transcription is ensured, are still mostly unclear. By combining misexpression assays with CRM analyses, we have identified the mechanisms through which Ciona Macho1 (Ci-Macho1) initiates expression of Ci-Tbx6b and Ci-Tbx6c, and we have unveiled the cross-regulatory interactions between the latter transcription factors. Knowledge acquired from the analysis of the Ci-Tbx6b CRM facilitated both the identification of a related CRM in the Ci-Tbx6c locus and the characterization of two CRMs associated with the structural muscle gene fibrillar collagen 1 (CiFCol1). We use these representative examples to reconstruct how compact CRMs orchestrate the muscle developmental program from pre-localized ooplasmic determinants to differentiated larval muscle in ascidian embryos

A Model of Proto-Anti-Codon RNA Enzymes Requiring l-Amino Acid Homochirality

All living organisms encode the 20 natural amino acid units of polypeptides using a universal scheme of triplet nucleotide “codons”. Disparate features of this codon scheme are potentially informative of early molecular evolution: (i) the absence of any codons for d-amino acids; (ii) the odd combination of alternate codon patterns for some amino acids; (iii) the confinement of synonymous positions to a codon’s third nucleotide; (iv) the use of 20 specific amino acids rather than a number closer to the full coding potential of 64; and (v) the evolutionary relationship of patterns in stop codons to amino acid codons. Here I propose a model for an ancestral proto-anti-codon RNA (pacRNA) auto-aminoacylation system and show that pacRNAs would naturally manifest features of the codon table. I show that pacRNAs could implement all the steps for auto-aminoacylation: amino acid coordination, intermediate activation of the amino acid by the 5′-end of the pacRNA, and 3′-aminoacylation of the pacRNA. The anti-codon cradles of pacRNAs would have been able to recognize and coordinate only a small number of l-amino acids via hydrogen bonding. A need for proper spatial coordination would have limited the number of chargeable amino acids for all anti-codon sequences, in addition to making some anti-codon sequences unsuitable. Thus, the pacRNA model implies that the idiosyncrasies of the anti-codon table and l-amino acid homochirality co-evolved during a single evolutionary period. These results further imply that early life consisted of an aminoacylated RNA world with a richer enzymatic potential than ribonucleotides alone

Phylogenetic analysis of the core histone doublet and DNA topo II genes of Marseilleviridae: evidence of proto-eukaryotic provenance

Abstract Background While the genomes of eukaryotes and Archaea both encode the histone-fold domain, only eukaryotes encode the core histone paralogs H2A, H2B, H3, and H4. With DNA, these core histones assemble into the nucleosomal octamer underlying eukaryotic chromatin. Importantly, core histones for H2A and H3 are maintained as neofunctionalized paralogs adapted for general bulk chromatin (canonical H2 and H3) or specialized chromatin (H2A.Z enriched at gene promoters and cenH3s enriched at centromeres). In this context, the identification of core histone-like “doublets” in the cytoplasmic replication factories of the Marseilleviridae (MV) is a novel finding with possible relevance to understanding the origin of eukaryotic chromatin. Here, we analyze and compare the core histone doublet genes from all known MV genomes as well as other MV genes relevant to the origin of the eukaryotic replisome. Results Using different phylogenetic approaches, we show that MV histone domains encode obligate H2B-H2A and H4-H3 dimers of possible proto-eukaryotic origin. MV core histone moieties form sister clades to each of the four eukaryotic clades of canonical and variant core histones. This suggests that MV core histone moieties diverged prior to eukaryotic neofunctionalizations associated with paired linear chromosomes and variant histone octamer assembly. We also show that MV genomes encode a proto-eukaryotic DNA topoisomerase II enzyme that forms a sister clade to eukaryotes. This is a relevant finding given that DNA topo II influences histone deposition and chromatin compaction and is the second most abundant nuclear protein after histones. Conclusions The combined domain architecture and phylogenomic analyses presented here suggest that a primitive origin for MV histone genes is a more parsimonious explanation than horizontal gene transfers + gene fusions + sufficient divergence to eliminate relatedness to eukaryotic neofunctionalizations within the H2A and H3 clades without loss of relatedness to each of the four core histone clades. We thus suggest MV histone doublet genes and their DNA topo II gene possibly were acquired from an organism with a chromatinized replisome that diverged prior to the origin of eukaryotic core histone variants for H2/H2A.Z and H3/cenH3. These results also imply that core histones were utilized ancestrally in viral DNA compaction and/or protection from host endonucleases

Evolving Notch polyQ tracts reveal possible solenoid interference elements

<div><p>Polyglutamine (polyQ) tracts in regulatory proteins are extremely polymorphic. As functional elements under selection for length, triplet repeats are prone to DNA replication slippage and indel mutations. Many polyQ tracts are also embedded within intrinsically disordered domains, which are less constrained, fast evolving, and difficult to characterize. To identify structural principles underlying polyQ tracts in disordered regulatory domains, here I analyze deep evolution of metazoan Notch polyQ tracts, which can generate alleles causing developmental and neurogenic defects. I show that Notch features polyQ tract turnover that is restricted to a discrete number of conserved “polyQ insertion slots”. Notch polyQ insertion slots are: (<i>i</i>) identifiable by an amphipathic “slot leader” motif; (<i>ii</i>) conserved as an intact C-terminal array in a 1-to-1 relationship with the N-terminal solenoid-forming ankyrin repeats (ARs); and (<i>iii</i>) enriched in carboxamide residues (Q/N), whose sidechains feature dual hydrogen bond donor and acceptor atoms. Correspondingly, the terminal loop and β-strand of each AR feature conserved carboxamide residues, which would be susceptible to folding interference by hydrogen bonding with residues outside the ARs. I thus suggest that Notch polyQ insertion slots constitute an array of AR interference elements (ARIEs). Notch ARIEs would dynamically compete with the delicate serial folding induced by adjacent ARs. Huntingtin, which harbors solenoid-forming HEAT repeats, also possesses a similar number of polyQ insertion slots. These results suggest that intrinsically disordered interference arrays featuring carboxamide and polyQ enrichment may constitute coupled proteodynamic modulators of solenoids.</p></div

PolyQ tracts evolve in well-defined slots in Htt and Notch proteins.

<p><b>(a)</b> Shown is the N-terminal region of Huntingtin (Htt) from humans, tarsier, mouse, and <i>Drosophila</i>. This region evolved a polyglutamine (polyQ) tract at a well-defined location in mammals, which later expanded in the evolution of humans, and is still evolving. While fly Htt is missing the N-terminal polyQ tract, it features a separate tract elsewhere in the protein as shown. Small amino acid residues that are secondary structure breakers are highlighted in blue. Glutamine residues are highlighted in red. Hydrophobic amino acid residues preceding the polyQ tract insertion site are highlighted in cyan. Conserved residues are highlighted in yellow. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174253#pone.0174253.g003" target="_blank">Fig 3</a> for a diagram showing the location of polyQ tracts relative to other NICD domains. <b>(b)</b> Shown is an evolutionary tree of various dipteran genera for which Notch sequences were analyzed in this study. The cladogram is a simplified version of the comprehensive fly tree based on multiple nuclear and mitochondrial genes and morphological markers [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174253#pone.0174253.ref042" target="_blank">42</a>]. The six different families to which these species belong are listed. <b>(c)</b> Shown is the polyQ tract regions of fly Notch proteins. Several sites (lettered slots) have independently evolved a polyQ tract in different fly genera. Most slots are preceded by a leader motif sequence, even when a polyQ tract is not present. <b>(d)</b> Inset shows the high hydrogen bonding potential of carboxamide amino acid side chains.</p

Notch AR interference elements (ARIEs) are present as a distinct array within NICD.

<p><b>(a)</b> The polyQ slot leader motif defines 7 possible insertion sites, for which six have independently evolved polyQ tracts in distinct lineages of flies. The number of slots is also suggestive of an interference with the seven ankyrin repeats or the six pairs of adjacent repeats. <b>(b)</b> The leader sequences from <i>Drosophila</i> and <i>Stomoxys</i> polyQ insertion slots (except for slot C) were used to produce the motif logo shown. Also shown is an amphipathic helix starting with residue number four and showing how the hydrophobic amino acids at positions 6, 9, and 10 of the slot leader motif are segregated to one side of the helix (yellow circles). Interestingly, position 7 frequently features a single glutamine residue, which could interact with an adjacent polyQ tract. <b>(c)</b> <i>Drosophila</i> Notch and vertebrate Notch1 feature a polyQ tract in slot-G, although it is much more expanded in <i>Drosophila</i> than humans. <b>(d, e)</b> Unlike <i>Drosophila</i> Notch, the Notch proteins from several other fly genera, including <i>Musca</i>, <i>Stomoxys</i>, <i>Glossina</i>, <i>Lucilia</i>, <i>Bactrocera</i>, and <i>Ceratitis</i>, feature a more prominent polyQ tract in slot-F. These flies also have a much smaller polyQ tract in slot-G. The tephritid genera also feature a tract in slot-A, demonstrating that N-terminal slots can also accept polyQ tracts. <b>(f)</b> The Notch protein from <i>Anopheles darlingii</i> features polyQ tracts in slot-B and slot-E in addition to a very long tract in slot-G.</p

A perfect HSE4 element is specific to a <i>clpB</i> refolding regulon in <i>S</i>. <i>cerevisiae</i>.

<p>Abbreviations: DP-I, dot plot motif I; IUPAC, International Union of Pure and Applied Chemistry; PWM, Position-Weighted Matrix; Ψ, pseudo-count correction.</p><p>* Models 1–3 describe the genomic distributions of the <i>clpB</i>-specific HSE4 element using different descriptions. IUPAC DNA codes are used as needed except ‘N’ is represented by a dot (‘.’). Y = pYrimidine (C or T), and R = puRine (A or G).</p><p>** Percentages refer to the fraction of all genomic loci matching the model signature that are known to be involved in prion homeostasis. All such loci are listed in bold in the penultimate column. Hits in CDS regions are not listed but are counted for the precision metric.</p><p>A perfect HSE4 element is specific to a <i>clpB</i> refolding regulon in <i>S</i>. <i>cerevisiae</i>.</p