Fast sequence evolution of Hox and Hox -derived genes in the genus Drosophila

Background  

It is expected that genes that are expressed early in development and have a complex expression pattern are under strong purifying selection and thus evolve slowly. Hox genes fulfill these criteria and thus, should have a low evolutionary rate. However, some observations point to a completely different scenario. Hox genes are usually highly conserved inside the homeobox, but very variable outside it.     

Hox genes and the regulation of movement in Drosophila

Many animals show regionally specialized patterns of movement along the body axis. In vertebrates, spinal networks regulate locomotion, while the brainstem controls movements of respiration and feeding. Similarly, amongst invertebrates diversification of appendages along the body axis is tied to the performance of characteristically different movements such as those required for feeding, locomotion, and respiration. Such movements require locally specialized networks of nerves and muscles. Here we use the regionally differentiated movements of larval crawling in Drosophila to investigate how the formation of a locally specialized locomotor network is genetically determined. By loss and gain of function experiments we show that particular Hox gene functions are necessary and sufficient to dictate the formation of a neuromuscular network that orchestrates the movements of peristaltic locomotion.     

Adaptive evolution of newly emerged micro-RNA genes in Drosophila

How often micro-RNA (miRNA) genes emerged and how fast theyevolved soon after their emergence are some of the central questionsin the evolution of miRNAs. Because most known miRNA genes areancient and highly conserved, these questions can be best answeredby identifying newly emerged miRNA genes. Among the 78 miRNAgenes in Drosophila reported before 2007, only 5 are confirmedto be newly emerged in the genus (although many more can befound in the newly reported data set; e.g., Ruby et al. 2007;Stark et al. 2007; Lu et al. 2008). These new miRNA genes haveundergone numerous changes, even in the normally invariant maturesequences. Four of them (the miR-310/311/312/313 cluster, denotedmiR-310s) were duplicated from other conserved miRNA genes.The fifth one (miR-303) appears to be a very young gene, originatingde novo from a non-miRNA sequence recently. We sequenced these5 miRNA genes and their neighboring regions from a worldwidecollection of Drosophila melanogaster lines. The levels of divergenceand polymorphism in these miRNA genes, vis-à-vis thoseof the neighboring DNA sequences, suggest that these 5 genesare evolving adaptively. Furthermore, the polymorphism patternof miR-310s in D. melanogaster is indicative of hitchhikingunder positive selection. Thus, a large number of adaptive changesover a long period of time may be essential for the evolutionof newly emerged miRNA genes.     

Roles of Hox genes in the patterning of the central nervous system of Drosophila

One of the key aspects of functional nervous systems is the restriction of particular neural subtypes to specific regions, which permits the establishment of differential segment-specific neuromuscular networks. Although Hox genes play a major role in shaping the anterior-posterior body axis during animal development, our understanding of how they act in individual cells to determine particular traits at precise developmental stages is rudimentary. We have used the abdominal leucokinergic neurons (ABLKs) to address this issue. These neurons are generated during both embryonic and postembryonic neurogenesis by the same progenitor neuroblast, and are designated embryonic and postembryonic ABLKs, respectively. We report that the genes of the Bithorax-Complex, Ultrabithorax (Ubx) and abdominal-A (abd-A) are redundantly required to specify the embryonic ABLKs. Moreover, the segment-specific pattern of the postembryonic ABLKs, which are restricted to the most anterior abdominal segments, is controlled by the absence of Abdominal-B (Abd-B), which we found was able to repress the expression of the neuropeptide leucokinin. We discuss this and other examples of how Hox genes generate diversity within the central nervous system of Drosophila.Keyword: development, Hox genes, central nervous system, Drosophila, cell fate specification     

Cellular organelles facilitate dimerization of a newly identified Arf from Chlamydomonas reinhardtii

GTPases of the Ras superfamily regulate a wide variety of cellular processes including vesicular transport and various secretory pathways of the cell. ADP – ribosylation factor (ARF) belongs to one of the five major families of the Ras superfamily and serves as an important component of vesicle formation and transport machinery of the cells. The binding of GTP to these Arfs and its subsequent hydrolysis, induces conformational changes in these proteins leading to their enzymatic activities. The dimeric form of Arf is associated with membrane pinch‐off during vesicle formation. In this report, we have identified an arf gene from the unicellular green alga Chlamydomonas reinhardtii, CrArf, and showed that the oligomeric state of the protein in C. renhardtii is modulated by the cellular membrane environment of the organism. Protein cross‐linking experiments showed that the purified recombinant CrArf has the ability to form a dimer. Both the 20‐kDa monomeric and 40‐kDa dimeric forms of CrArf were recognized from Chlamydomonas total cell lysate (CrTLC) and purified recombinant CrArf by the CrArf specific antibody. The membranous environment of the cell appeared to facilitate dimerization of the CrArf, as dimeric form was found exclusively associated with the membrane bound organelles. The subcellular localization studies in Chlamydomonas suggested that CrArf mainly localized in the cytosol and was mislocalized in vesicle transport machinery inhibitor treated cells. This research sheds light on the importance of the cellular membrane environment for regulating the oligomeric state of CrArf protein in this organism and associated functional role.     

Two more Posterior Hox genes and Hox cluster dispersal in echinoderms

Background

Hox genes are key elements in patterning animal development. They are renowned for their, often, clustered organisation in the genome, with supposed mechanistic links between the organisation of the genes and their expression. The widespread distribution and comparable functions of Hox genes across the animals has led to them being a major study system for comparing the molecular bases for construction and divergence of animal morphologies. Echinoderms (including sea urchins, sea stars, sea cucumbers, feather stars and brittle stars) possess one of the most unusual body plans in the animal kingdom with pronounced pentameral symmetry in the adults. Consequently, much interest has focused on their development, evolution and the role of the Hox genes in these processes. In this context, the organisation of echinoderm Hox gene clusters is distinctive. Within the classificatory system of Duboule, echinoderms constitute one of the clearest examples of Disorganized (D) clusters (i.e. intact clusters but with a gene order or orientation rearranged relative to the ancestral state).

Results

Here we describe two Hox genes (Hox11/13d and e) that have been overlooked in most previous work and have not been considered in reconstructions of echinoderm Hox complements and cluster organisation. The two genes are related to Posterior Hox genes and are present in all classes of echinoderm. Importantly, they do not reside in the Hox cluster of any species for which genomic linkage data is available.

Conclusion

Incorporating the two neglected Posterior Hox genes into assessments of echinoderm Hox gene complements and organisation shows that these animals in fact have Split (S) Hox clusters rather than simply Disorganized (D) clusters within the Duboule classification scheme. This then has implications for how these genes are likely regulated, with them no longer covered by any potential long-range Hox cluster-wide, or multigenic sub-cluster, regulatory mechanisms.

     

Hox genes in a pentameral animal

There is renewed interest in how the different body plans of extant phyla are related. This question has traditionally been addressed by comparisons between vertebrates and Drosophila. Fortunately, there is now increasing emphasis on animals representing other phyla. Pentamerally symmetric echinoderms are a bilaterian metazoan phylum whose members exhibit secondarily derived radial symmetry. Precisely how their radially symmetric body plan originated from a bilaterally symmetric ancestor is unknown, however, two recent papers address this subject. Peterson et al. propose a hypothesis on evolution of the anteroposterior axis in echinoderms, and Arenas-Mena et al. examine expression of five posterior Hox genes during development of the adult sea urchin.     

Neuronal expression of a newly identified Drosophila melanogaster G protein alpha 0 subunit.

Guanine nucleotide-binding proteins (G proteins) mediate signals between activated cell-surface receptors and cellular effectors. A bovine G-protein alpha-subunit cDNA has been used to isolate similar sequences from Drosophila genomic and cDNA libraries. One class, which we call DG alpha 0, hybridized to position 47A on the second chromosome of Drosophila. The nucleotide sequence of the protein coding region of one cDNA has been determined, revealing an alpha subunit that is 81% identical with rat alpha 0. The cDNA hybridizes strongly to a 3.8 kb mRNA and weakly with a 5.3 kb message. Antibodies raised against a trp-E-DG alpha 0 fusion protein recognized a 39,000 Da protein in Drosophila extracts. In situ hybridization to adult Drosophila sections combined with immunohistochemical studies revealed expression throughout the optic lobes and central brain and in the thoracic and abdominal ganglia. DG alpha 0 message and protein were also detected in the antennae, oocytes, and ovarian nurse cells. The neuronal expression of this gene is similar to mammalian alpha 0, which is most abundantly expressed in the brain.