Genetic and biochemical interactions between the bacterial replication initiator DnaA and the nucleoid-associated protein Rok in Bacillus subtilis.

We identified interactions between the conserved bacterial replication initiator and transcription factor DnaA and the nucleoid-associated protein Rok of Bacillus subtilis. DnaA binds directly to clusters of DnaA boxes at the origin of replication and elsewhere, including the promoters of several DnaA-regulated genes. Rok, an analog of H-NS from gamma-proteobacteria that affects chromosome architecture and of Lsr2 from Mycobacteria, binds A+T-rich sequences throughout the genome and represses expression of many genes. Using crosslinking and immunoprecipitation followed by deep sequencing (ChIP-seq), we found that DnaA was associated with eight previously identified regions containing clusters of DnaA boxes, plus 36 additional regions that were also bound by Rok. Association of DnaA with these additional regions appeared to be indirect as it was dependent on Rok and independent of the DNA-binding domain of DnaA. Gene expression and mutant analyses support a model in which DnaA and Rok cooperate to repress transcription of yxaJ, the yybNM operon and the sunA-bdbB operon. Our results indicate that DnaA modulates the activity of Rok. We postulate that this interaction might affect nucleoid architecture. Furthermore, DnaA might interact similarly with Rok analogues in other organisms.

Spatial tethering of kinases to their substrates relaxes evolutionary constraints on specificity.

Signal transduction proteins are often multi-domain proteins that arose through the fusion of previously independent proteins. How such a change in the spatial arrangement of proteins impacts their evolution and the selective pressures acting on individual residues is largely unknown. We explored this problem in the context of bacterial two-component signalling pathways, which typically involve a sensor histidine kinase that specifically phosphorylates a single cognate response regulator. Although usually found as separate proteins, these proteins are sometimes fused into a so-called hybrid histidine kinase. Here, we demonstrate that the isolated kinase domains of hybrid kinases exhibit a dramatic reduction in phosphotransfer specificity in vitro relative to canonical histidine kinases. However, hybrid kinases phosphotransfer almost exclusively to their covalently attached response regulator domain, whose effective concentration exceeds that of all soluble response regulators. These findings indicate that the fused response regulator in a hybrid kinase normally prevents detrimental cross-talk between pathways. More generally, our results shed light on how the spatial properties of signalling pathways can significantly affect their evolution, with additional implications for the design of synthetic signalling systems.

A new deep-sea eelpout of the genus Pyrolycus (Teleostei: Zoarcidae) associated with a hydrothermal seep on the Pacific margin of Costa Rica.

A new species of the zoarcid genus Pyrolycus Machida & Hashimoto, 2002, Pyrolycus jaco sp. nov., is described from a hydrothermal seep environment named Jacó Scar in the eastern Pacific of Costa Rica. Four specimens were collected in 2018 between 1746-1795 m among tubeworm colonies around the seep. The new species is differentiated from its two western Pacific congeners by having a shorter head, snout, jaw, and pectoral fins. It is further diagnosed by having three postorbital pores and two occipital pores. Molecular sequences of the cytochrome c oxidase I gene are provided and are the first for the genus. The character states indicating miniaturization in this species are discussed. This is the first vertebrate species known from this composite reducing ecosystem and is the fourth hydrothermally-associated zoarcid from the eastern Pacific.

Range extensions of Pacific bone-eating worms (Annelida, Siboglinidae, Osedax).

First described in 2004 off California, Osedax worms are now known from many of the world's oceans, ranging from 10 to over 4000 m in depth. Currently, little is known about species ranges, since most descriptions are from single localities. In this study, we used new sampling in the north-eastern Pacific and available GenBank data from off Japan and Brazil to report expanded ranges for five species: Osedaxfrankpressi, O.knutei, O.packardorum, O.roseus and O.talkovici. We also provided additional DNA sequences from previously reported localities for two species: Osedaxpriapus and O.randyi. To assess the distribution of each species, we used cytochrome c oxidase subunit I (COI) sequences to generate haplotype networks and assess connectivity amongst localities where sampling permitted. Osedaxfrankpressi, O.packardorum, O.priapus, O.roseus and O.talkovici all had one or more dominant COI haplotypes shared by individuals at multiple localities, suggesting high connectivity throughout some or all of their ranges. Low ΦST values amongst populations for O.packardorum, O.roseus and O.talkovici confirmed high levels of gene flow throughout their known ranges. High ΦST values for O.frankpressi between the eastern Pacific and the Brazilian Atlantic showed little gene flow, reflected by the haplotype network, which had distinct Pacific and Atlantic haplotype clusters. This study greatly expands the ranges and provides insights into the phylogeography for these nine species.

Comparative analysis of genome-scale, base-resolution DNA methylation profiles across 580 animal species.

Methylation of cytosines is a prototypic epigenetic modification of the DNA. It has been implicated in various regulatory mechanisms across the animal kingdom and particularly in vertebrates. We mapped DNA methylation in 580 animal species (535 vertebrates, 45 invertebrates), resulting in 2443 genome-scale DNA methylation profiles of multiple organs. Bioinformatic analysis of this large dataset quantified the association of DNA methylation with the underlying genomic DNA sequence throughout vertebrate evolution. We observed a broadly conserved link with two major transitions-once in the first vertebrates and again with the emergence of reptiles. Cross-species comparisons focusing on individual organs supported a deeply conserved association of DNA methylation with tissue type, and cross-mapping analysis of DNA methylation at gene promoters revealed evolutionary changes for orthologous genes. In summary, this study establishes a large resource of vertebrate and invertebrate DNA methylomes, it showcases the power of reference-free epigenome analysis in species for which no reference genomes are available, and it contributes an epigenetic perspective to the study of vertebrate evolution.

A new southern record of the holopelagic annelid Poeobius meseres Heath, 1930 (Flabelligeridae).

BACKGROUND: The unusual holopelagic annelid Poeobius meseres Heath, 1930 (Flabelligeridae) was first collected from Monterey Bay, California and has been subsequently recorded across the northern Pacific from Japan to the Gulf of California. Rare occurrences in the eastern tropical Pacific have extended as far as 7° S off Peru. NEW INFORMATION: Using molecular phylogenetic analysis of a newly-collected specimen from the Salas y Gómez Ridge off Chile, we extend the known geographic range of P. meseres southwards by 2040 km. This subtropical specimen showed higher genetic similarity to a specimen from the type locality (< 1.5% pairwise COI distance) than to representatives from the Aleutian Islands and Japan (5-6%), establishing the first genetically-confirmed occurrence of this species in the Southern Hemisphere. The latitudinal range of P. meseres encompasses the sole collection locality, off Ecuador, of Enigma terwielii Betrem, 1925, a pelagic annelid which has been compared to P. meseres, but is indeterminable due to an inadequate description. We therefore suggest that the earlier sole record of E. terwielii may have been an occurrence of what is known now as P. meseres.

A new species of Alvinocaris (Crustacea: Decapoda: Caridea: Alvinocarididae) from Costa Rican methane seeps.

A new caridean shrimp, Alvinocaris costaricensis, is described from methane seeps in the eastern Pacific off Costa Rica. The new species is the 16th described species of the genus, and by molecular analysis appears closest to Alvinocaris komaii from the Lau Basin, southwestern Pacific, but shares certain morphological characters with A. lusca from the Galapagos Rift and A. muricola from the West Florida Escarpment, as well as with A. kexueae from the Manus Basin in the Southwest Pacific.