Abstract
Haloferax volcanii, a well-developed model archaeon for genomic, transcriptomic, and proteomic analyses, can grow on a defined medium of abundant and intermediate levels of fixed nitrogen. Here we report a global profiling of gene expression of H. volcanii grown on ammonium as an abundant source of fixed nitrogen compared to l-alanine, the latter of which exemplifies an intermediate source of nitrogen that can be obtained from dead cells in natural habitats. By comparing the two growth conditions, 30 genes were found to be differentially expressed, including 16 genes associated with amino acid metabolism and transport. The gene expression profiles contributed to mapping ammonium and l-alanine usage with respect to transporters and metabolic pathways. In addition, conserved DNA motifs were identified in the putative promoter regions and transcription factors were found to be in synteny with the differentially expressed genes, leading us to propose regulons of transcriptionally co-regulated operons. This study provides insight to how H. volcanii responds to and utilizes intermediate vs. abundant sources of fixed nitrogen for growth, with implications for conserved functions in related halophilic archaea.
Highlights
Transcription is a primary mechanism that enables organisms to regulate gene expression to produce cellular factors in response to changing environmental conditions
H. volcanii H26 strain was analyzed for growth on glycerol minimal medium (GMM) with the N-source of 10 mM ammonium chloride or 10 mM l-alanine
Model of metabolic and transport shifts that occur when glycerol grown H. volcanii cells use LF3igureal4an. iMneoidnsetleaodf mofeatmabmoolniciuamndastraannNsp-soorutrcseh. ifRtesatchtioantsoacrceurdewfinheednignlythceerToalbgleroinwsent Hwi.thvotlhcoasneii cells use l-4alanhinigehlinghstteedadinogfreaemn masosonciautmed awsitahntrNan-sscoriuprtsceth. aRt eaarectmioonres abreunddeafintnoend Li-naltahnieneTacbomlepianresdettowith those h5ighliagmhmteodniiunmg. *r,ereefneraenscseoicsisapteecdificwfoitrhHatlroafenrasxcsrpip. ts that are more abundant on l-alanine compared to ammonium. *, reference is specific for Haloferax sp. [46,47,48,49,50,51,52,53,54,55]
Summary
Transcription is a primary mechanism that enables organisms to regulate gene expression to produce cellular factors in response to changing environmental conditions. Global transcriptional analyses using expression microarray, and most recently RNA-seq, are widely used to analyze the gene expression level of bacteria and eukaryotes in response to various stimuli and environmental conditions [3,4,5,6]. One of the most common elements on the earth, is present in different redox states from nitrate (NO3−) to ammonium (NH4+). Considering that N-cycle compounds impact natural environments (e.g., N2O is a potent greenhouse gas) and human health (e.g., nitrate consumption is relevant to cancer and adverse reproductive outcomes), better understanding of nitrogen metabolism across diverse microbial groups will inform on the role of different environments in the global N-cycle [18,19]
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