Abstract
Two-component signal transduction systems (TCSs) are a major mechanism used by bacteria in response to environmental changes. Although many sequenced archaeal genomes encode TCSs, they remain poorly understood. Previously, we reported that a methanogenic archaeon, Methanosaeta harundinacea, encodes FilI, which synthesizes carboxyl-acyl homoserine lactones, to regulate transitions of cellular morphology and carbon metabolic fluxes. Here, we report that filI, the cotranscribed filR2, and the adjacent filR1 constitute an archaeal TCS. FilI possesses a cytoplasmic kinase domain (histidine kinase A and histidine kinase-like ATPase) and its cognate response regulator. FilR1 carries a receiver (REC) domain coupled with an ArsR-related domain with potential DNA-binding ability, while FilR2 carries only a REC domain. In a phosphorelay assay, FilI was autophosphorylated and specifically transferred the phosphoryl group to FilR1 and FilR2, confirming that the three formed a cognate TCS. Through chromatin immunoprecipitation–quantitative polymerase chain reaction (ChIP-qPCR) using an anti-FilR1 antibody, FilR1 was shown to form in vivo associations with its own promoter and the promoter of the filI-filR2 operon, demonstrating a regulatory pattern common among TCSs. ChIP-qPCR also detected FilR1 associations with key genes involved in acetoclastic methanogenesis, acs4 and acs1. Electrophoretic mobility shift assays confirmed the in vitro tight binding of FilR1 to its own promoter and those of filI-filR2, acs4, and mtrABC. This also proves the DNA-binding ability of the ArsR-related domain, which is found primarily in Archaea. The archaeal promoters of acs4, filI, acs1, and mtrABC also initiated FilR1-modulated expression in an Escherichia coli lux reporter system, suggesting that FilR1 can up-regulate both archaeal and bacterial transcription. In conclusion, this work identifies an archaeal FilI/FilRs TCS that regulates the methanogenesis of M. harundinacea.
Highlights
Methanogenesis is a major contributor to global warming, and methanogens are the only organisms known to perform this metabolism [1]
To gain a general view of the transduction systems (TCSs) in M. harundinacea 6Ac, bacterial prototypical kinase core domains of histidine kinase (HK) and REC core domains of RRs were used as probes to query the genome (CP003117) [17]
TCSs are distributed widely in bacteria and are well characterized [7,14,19]. They are abundant in free-living species like E. coli and Bacillus subtilis, which contain 30 and 36 TCSs [19], respectively, but they are absent in many parasites, such as Mycoplasma genitalium and Mycoplasma pneumonia [14,15]
Summary
Methanogenesis is a major contributor to global warming, and methanogens are the only organisms known to perform this metabolism [1]. Acetate-derived methane contributes about 70% of the global methane production and is produced by acetoclastic methanogens such as Methanosarcina and Methanosaeta. These archaea possess prokaryotic cells, their genetic machinery for replication, transcription, and translation more closely resembles that of Eukarya than Bacteria [2]. Gao and Stock summarized the diverse bacterial TCSs, indicating that the typical TCS comprises a membranebound sensor histidine kinase (HK) and a cognate response regulator (RR) and catalyzes a phosphotransfer between the two [8]. Upon sensing environmental stimuli, the HK is autophosphorylated at a conserved histidine residue. Approximately 17% of RRs exist as standalone REC domains that lack an effector domain [8,10,11]; these RRs usually implement a more intricate regulation of a TCS [12,13]
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