The Early Evolution of Hox Genes: A Battle of Belief?

FgHtf1 Regulates Global Gene Expression towards Aerial Mycelium and Conidiophore Formation in the Cereal Fungal Pathogen Fusarium graminearum

The homeobox gene family of transcription factors (HTF) controls many developmental pathways and physiological processes in eukaryotes. We previously showed that a conserved HTF in the plant-pathogenic fungus Fusarium graminearum, Htf1 (FgHtf1), regulates conidium morphology in that organism. This study investigated the mechanism of FgHtf1-mediated regulation and identified putative FgHtf1 target genes by a chromatin immunoprecipitation assay combined with parallel DNA sequencing (ChIP-seq) and RNA sequencing. A total of 186 potential binding peaks, including 142 genes directly regulated by FgHtf1, were identified. Subsequent motif prediction analysis identified two DNA-binding motifs, TAAT and CTTGT. Among the FgHtf1 target genes were FgHTF1 itself and several important conidiation-related genes (e.g., FgCON7), the chitin synthase pathway genes, and the aurofusarin biosynthetic pathway genes. In addition, FgHtf1 may regulate the cAMP-protein kinase A (PKA)-Msn2/4 and Ca²⁺-calcineurin-Crz1 pathways. Taken together, these results suggest that, in addition to autoregulation, FgHtf1 also controls global gene expression and promotes a shift to aerial growth and conidiation in F. graminearum by activation of FgCON7 or other conidiation-related genes.IMPORTANCE The homeobox gene family of transcription factors is known to be involved in the development and conidiation of filamentous fungi. However, the regulatory mechanisms and downstream targets of homeobox genes remain unclear. FgHtf1 is a homeobox transcription factor that is required for phialide development and conidiogenesis in the plant pathogen F. graminearum In this study, we identified FgHtf1-controlled target genes and binding motifs. We found that, besides autoregulation, FgHtf1 also controls global gene expression and promotes conidiation in F. graminearum by activation of genes necessary for aerial growth, FgCON7, and other conidiation-related genes.

Bacterial DNA sifted from the Trichoplax adhaerens (Animalia: Placozoa) genome project reveals a putative rickettsial endosymbiont

Eukaryotic genome sequencing projects often yield bacterial DNA sequences, data typically considered as microbial contamination. However, these sequences may also indicate either symbiont genes or lateral gene transfer (LGT) to host genomes. These bacterial sequences can provide clues about eukaryote-microbe interactions. Here, we used the genome of the primitive animal Trichoplax adhaerens (Metazoa: Placozoa), which is known to harbor an uncharacterized Gram-negative endosymbiont, to search for the presence of bacterial DNA sequences. Bioinformatic and phylogenomic analyses of extracted data from the genome assembly (181 bacterial coding sequences [CDS]) and trace read archive (16S rDNA) revealed a dominant proteobacterial profile strongly skewed to Rickettsiales (Alphaproteobacteria) genomes. By way of phylogenetic analysis of 16S rDNA and 113 proteins conserved across proteobacterial genomes, as well as identification of 27 rickettsial signature genes, we propose a Rickettsiales endosymbiont of T. adhaerens (RETA). The majority (93%) of the identified bacterial CDS belongs to small scaffolds containing prokaryotic-like genes; however, 12 CDS were identified on large scaffolds comprised of eukaryotic-like genes, suggesting that T. adhaerens might have recently acquired bacterial genes. These putative LGTs may coincide with the placozoan's aquatic niche and symbiosis with RETA. This work underscores the rich, and relatively untapped, resource of eukaryotic genome projects for harboring data pertinent to host-microbial interactions. The nature of unknown (or poorly characterized) bacterial species may only emerge via analysis of host genome sequencing projects, particularly if these species are resistant to cell culturing, as are many obligate intracellular microbes. Our work provides methodological insight for such an approach.

Deep proteome profiling of Trichoplax adhaerens reveals remarkable features at the origin of metazoan multicellularity

Genome sequencing of arguably the simplest known animal, Trichoplax adhaerens, uncovered a rich array of transcription factor and signalling pathway genes. Although the existence of such genes allows speculation about the presence of complex regulatory events, it does not reveal the level of actual protein expression and functionalization through posttranslational modifications. Using high-resolution mass spectrometry, we here semi-quantify 6,516 predicted proteins, revealing evidence of horizontal gene transfer and the presence at the protein level of nodes important in animal signalling pathways. Moreover, our data demonstrate a remarkably high activity of tyrosine phosphorylation, in line with the hypothesized burst of tyrosine-regulated signalling at the instance of animal multicellularity. Together, this Trichoplax proteomics data set offers significant new insight into the mechanisms underlying the emergence of metazoan multicellularity and provides a resource for interested researchers.

Novel scenarios of early animal evolution--is it time to rewrite textbooks?

Understanding how important phenotypic, developmental, and genomic features of animals originated and evolved is essential for many fields of biological research, but such understanding depends on robust hypotheses about the phylogenetic interrelationships of the higher taxa to which the studied species belong. Molecular approaches to phylogenetics have proven able to revolutionize our knowledge of organismal evolution. However, with respect to the deepest splits in the metazoan Tree of Life-the relationships between Bilateria and the four non-bilaterian phyla (Porifera, Placozoa, Ctenophora, and Cnidaria)-no consensus has been reached yet, since a number of different, often contradictory, hypotheses with sometimes spectacular implications have been proposed in recent years. Here, we review the recent literature on the topic and contrast it with more classical perceptions based on analyses of morphological characters. We conclude that the time is not yet ripe to rewrite zoological textbooks and advocate a conservative approach when it comes to developing scenarios of the early evolution of animals.

Coral comparative genomics reveal expanded Hox cluster in the cnidarian-bilaterian ancestor

The key developmental role of the Hox cluster of genes was established prior to the last common ancestor of protostomes and deuterostomes and the subsequent evolution of this cluster has played a major role in the morphological diversity exhibited in extant bilaterians. Despite 20 years of research into cnidarian Hox genes, the nature of the cnidarian-bilaterian ancestral Hox cluster remains unclear. In an attempt to further elucidate this critical phylogenetic node, we have characterized the Hox cluster of the recently sequenced Acropora digitifera genome. The A. digitifera genome contains two anterior Hox genes (PG1 and PG2) linked to an Eve homeobox gene and an Anthox1A gene, which is thought to be either a posterior or posterior/central Hox gene. These data show that the Hox cluster of the cnidarian-bilaterian ancestor was more extensive than previously thought. The results are congruent with the existence of an ancient set of constraints on the Hox cluster and reinforce the importance of incorporating a wide range of animal species to reconstruct critical ancestral nodes.

Isolation of Hox cluster genes from insects reveals an accelerated sequence evolution rate

Among gene families it is the Hox genes and among metazoan animals it is the insects (Hexapoda) that have attracted particular attention for studying the evolution of development. Surprisingly though, no Hox genes have been isolated from 26 out of 35 insect orders yet, and the existing sequences derive mainly from only two orders (61% from Hymenoptera and 22% from Diptera). We have designed insect specific primers and isolated 37 new partial homeobox sequences of Hox cluster genes (lab, pb, Hox3, ftz, Antp, Scr, abd-a, Abd-B, Dfd, and Ubx) from six insect orders, which are crucial to insect phylogenetics. These new gene sequences provide a first step towards comparative Hox gene studies in insects. Furthermore, comparative distance analyses of homeobox sequences reveal a correlation between gene divergence rate and species radiation success with insects showing the highest rate of homeobox sequence evolution.

Chasing the urmetazoon: striking a blow for quality data?

The ever-lingering question: "What did the urmetazoan look like?" has not lost its charm, appeal or elusiveness for one and a half centuries. A solid amount of organismal data give what some feel is a clear answer (e.g. Placozoa are at the base of the metazoan tree of life (ToL)), but a diversity of modern molecular data gives almost as many answers as there are exemplars, and even the largest molecular data sets could not solve the question and sometimes even suggest obvious zoological nonsense. Since the problems involved in this phylogenetic conundrum encompass a wide array of analytical freedom and uncertainty it seems questionable whether a further increase in molecular data (quantity) can solve this classical deep phylogeny problem. This review thus strikes a blow for evaluating quality data (including morphological, molecule morphologies, gene arrangement, and gene loss versus gene gain data) in an appropriate manner.