Biology subjects

Kloosterman, A.

Publications and source records attributed to Kloosterman, A..

3 recordsLinked to original sources

bioRxiv2024

Z-chromosome dosage compensation and a male-specific lncRNA in octopus

Sex chromosomes typically present as two copies of a large, gene-rich differentiated chromosome in the homogametic sex (e.g. XX in female mammals, ZZ in male birds) but as a single copy in the heterogametic sex, often paired with a sex-specific, degenerated chromosome (XY in male mammals, ZW in female birds). This creates a significant gene product dosage imbalance of the X and Z chromosomes between the sexes as well as between the single sex chromosome and the autosomes in the heterogametic sex, making its resolution essential. Dosage compensation and its molecular mechanisms have primarily been studied in select organisms, such as primates, rodents, birds, fruit flies, and Caenorhabditis elegans, while the extent and mechanisms of dosage compensation remain largely unexplored in the vast majority of animal taxa. Recently, coleoid cephalopods, including octopuses, squids, and cuttlefish, were reported to possess a ZZ/Z0 sex chromosome system1, where males carry two copies of the Z chromosome while females carry only one. However, whether dosage compensation occurs in these species remains unexplored. Here, we show, for the first time, that Z-chromosome dosage compensation is achieved in octopus. Using both original RNA-seq data from O.vulgaris paralarvae as well as publicly available datasets from O.vulgaris and O.sinensis, we report extensive but incomplete dosage compensation of the Z-chromosome in female octopus at the RNA level, similar to Z-chromosome dosage compensation in avian ZW systems. Furthermore, we identify two evolutionarily conserved Z-linked lncRNAs, one featuring strong male-biased expression patterns, that we termed "Zmast" and another with strong female-biased expression patterns that we termed "Zfest". Our results provide the first evidence of sex chromosome dosage compensation in octopus, representing one of the most ancient known animal sex-chromosome systems, and raise the possibility that non-coding RNA may play a role in its regulation, akin that observed in younger animal taxa.

molecular biology↗

bioRxiv2020

Competition sensing alters antibiotic production in Streptomyces

One of the most important ways that bacteria compete for resources and space is by producing antibiotics that inhibit competitors. Because antibiotic production is costly, the biosynthetic gene clusters coordinating their synthesis are under strict regulatory control and often require "elicitors" to induce expression, including cues from competing strains. Although these cues are common, they are not produced by all competitors and so the phenotypes causing induction remain unknown. By studying interactions between 24 antibiotic-producing streptomycetes we show that inhibition between competitors is common and occurs more frequently if strains are closely related. Next, we show that antibiotic production is more likely to be induced by cues from strains that are closely related or that share secondary metabolite biosynthetic gene clusters (BGCs). Unexpectedly, antibiotic production is less likely to be induced by competitors that inhibit the growth of a focal strain, indicating that cell damage is not a general cue for induction. In addition to induction, antibiotic production often decreased in the presence of a competitor, although this response was not associated with genetic relatedness or overlap in BGCs. Finally, we show that resource limitation increases the chance that antibiotic production declines during competion. Our results reveal the importance of social cues and resource availability in the dynamics of interference competition in streptomycetes. SIGNIFICANCE STATEMENTBacteria secrete antibiotics to inhibit their competitors, but the presence of competitors can determine whether these toxins are produced. Here, we study the role of the competitive and resource environment on antibiotic production in Streptomyces, bacteria renowned for their production of antibiotics. We show that Streptomyces are more likely to produce antibiotics when grown with closely related competitors or that share biosynthetic pathways for secondary metabolites, but not when they are threatened by competitors toxins, in contrast to predictions of the competition sensing hypothesis. Streptomyces also often reduce their output of antibiotics when grown with competitors, especially under nutrient limitation. Our findings highlight that interactions between the social and resource environments strongly regulate antibiotic production in these medicinally important bacteria.

microbiology↗

bioRxiv2018

Classification of the gifted natural product producer Streptomyces roseofaciens sp. nov. by polyphasic taxonomy

A novel verticillate strain of streptomycetes, Streptomyces strain MBT76T, was isolated from the QinLing mountains, which harbours more than 40 biosynthetic gene clusters for natural products. Here we present full taxonomic classification of strain MBT76T, and show that it has chemotaxonomic, genomic and morphological properties consistent with its classification in the genus Streptomyces. Strain MBT76T is part of the cluster of Streptoverticillates, a group within the genus Streptomyces that has characteristic whorl-forming spores produced in chains along the lateral wall of the hyphae. Multi-locus sequence analysis based on five housekeeping gene alleles showed that MBT76T is closely related to Streptomyces hiroshimensis. Average Nucleotide Identification (ANI) and Genome to Genome Distance Calculation (GGDC) of the genomes of strain MBT76T and S. hiroshimensis separated them into distinct species. Strain MBT76T represents a novel species of the genus Streptomyces for which we propose the name Streptomyces roseofaciens sp. nov. The type strain is MBT76T (=NCCB 100637T =DSM 106196T). The whole genome of MBT76T has 7974 predicted open reading frames and a total genome size of 8.64 Mb. Further genomic analysis showed that verticillate streptomycetes lack the sporulation gene ssgE, and our data suggest that this is a useful genetic marker for the spore-chain morphology of the verticillates.

microbiology↗