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Complex cellular differentiation in a haloarchaeon

ABSTRACT: Purpose: The goals of this study are to describe the morphological diversity of a novel archaea. Methods: The aerial and substrate hyphae of wild strain, and the substrate hyphae of mutated strains were generated by deep sequencing, in triplicate, using Illumina HiSeq2000 system. Results: Using an optimized data analysis workflow, we mapped about 1.7-4.4 million sequence reads per sample to wild and mutated hyphae samples by Bowti2 and RSeQC. Approximately half of the transcripts showed differential expression between the aerial and substrate hyphae, with a fold change ≥2.0 and p adjust <0.05. Conclusions: Our study represents the first detailed analysis of wild and mutated hyphae transcriptomes, with biologic replicates, generated by RNA-seq technology.

ORGANISM(S): Actinarchaeum halophilum

PROVIDER: GSE168067 | GEO | 2023/01/03

REPOSITORIES: GEO

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Project description:To gain insight into the targets of the PaMpk1 and PaMpk2 MAPK, we here determine the transcription profile of the mutants inactivated for PaMpk1, PaMpk2 and PaNox1 during vegetative growth at stages where they are required for proper development, in comparison with wild type. Microarrays representing 10556 coding sequences (CDS) predicted by the P. anserina genome project were used to estimate the transcription profiles (transcriptomes) during vegetative growth of three-day-old homokaryotic cultures of M-bM-^HM-^FPaMpk1, M-bM-^HM-^FPaMpk2 and the IDC343 PaNox1 mutants in comparison to wild type. Three zones corresponding to three developmental stages can be defined in such wild-type culture. From the growing edge the colony, the first five milimeters (zone 1) are constituted of hyphae lacking pigment and growing on the substrate. In this zone, very few hyphae are aerial and appressorium-like structures are not differentiated. In the second intermediate zone (zone 2), profuse aerial hyphae and appressorium-like structures are differentiated. This zone is about 7 mm wide and corresponds to the area where most perithecia are differentiated during sexual development of heterokaryotic mycelia. The zone that is most distal from the edge lack aerial hyphae (zone 3) accumulates a larger amount of pigment and differentiates few perithecia during sexual reproduction. It is about 1 cm wide. These three zones are easily visualized by the naked eye for sample recovery. The M-bM-^HM-^FPaMpk1, M-bM-^HM-^FPaMpk2 and the IDC343 PaNox1 mutants lack a clear zonation, since the three genes are involved in the signalling of stationary phase . Materials from these mutants were nonetheless recovered as three samples corresponding to the same zones, based mostly on the distance from the growing edge but also from subtle morphological differences. With GPL10116 : reference design, 4 strains (WT, M-bM-^HM-^FPaMpk1, M-bM-^HM-^FPaMpk2 and IDC343 PaNox1 with 3 growth conditions (zone1,2 and 3) each with four biological replicates, the common reference is a pool of four conditions M48h, M96h, C48h and C96h ; Conditions are labelled in Cy3 and the common reference in Cy5

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Complex cellular differentiation in a haloarchaeon

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