Bacterial nitrate assimilation: gene distribution and regulation

Abstract

In the context of the global nitrogen cycle, the importance of inorganic nitrate for the nutrition and growth of marine and freshwater autotrophic phytoplankton has long been recognized. In contrast, the utilization of nitrate by heterotrophic bacteria has historically received less attention because the primary role of these organisms has classically been considered to be the decomposition and mineralization of dissolved and particulate organic nitrogen. In the pre-genome sequence era, it was known that some, but not all, heterotrophic bacteria were capable of growth on nitrate as a sole nitrogen source. However, examination of currently available prokaryotic genome sequences suggests that assimilatory nitrate reductase (Nas) systems are widespread phylogenetically in bacterial and archaeal heterotrophs. Until now, regulation of nitrate assimilation has been mainly studied in cyanobacteria. In contrast, in heterotrophic bacterial strains, the study of nitrate assimilation regulation has been limited to Rhodobacter capsulatus, Klebsiella oxytoca, Azotobacter vinelandii and Bacillus subtilis. In Gram-negative bacteria, the nas genes are subjected to dual control: ammonia repression by the general nitrogen regulatory (Ntr) system and specific nitrate or nitrite induction. The Ntr system is widely distributed in bacteria, whereas the nitrate/nitrite-specific control is variable depending on the organism.

Nitrate Assimilation Contributes to Ralstonia solanacearum Root Attachment, Stem Colonization, and Virulence

“…This, together with the failure to detect any nasA transcript in the 5 mM ammonium condition, indicates that ammonium represses transcription of nitrate assimilation genes, as is typical in most nitrateassimilating bacteria (27). Growth in diluted tomato xylem sap, a biologically relevant condition, increased R. solanacearum nasA expression 16-fold (Fig.…”

“…The genomic structure of R. solanacearum's nitrate assimilation network is unique to a subset of Betaproteobacteria. Genomic analysis suggests R. solanacearum has two assimilatory nitrate uptake systems, encoded by nasFED and narK3 (26,27). The nasFED operon, predicted to encode the typical assimilatory nitrate transporter, is atypically distant from the metabolic operon, suggesting a relatively recent genomic rearrangement (27).…”

“…Genomic analysis suggests R. solanacearum has two assimilatory nitrate uptake systems, encoded by nasFED and narK3 (26,27). The nasFED operon, predicted to encode the typical assimilatory nitrate transporter, is atypically distant from the metabolic operon, suggesting a relatively recent genomic rearrangement (27). The metabolic operon is predicted to encode enzymes responsible for the reduction of nitrate and nitrite.…”

“…Entirely unique to R. solanacearum is the positioning of this operon between aer1 (encoding an energy taxis receptor [29]) and a cluster of predicted filamentous hemagglutinin genes. This nas operon has no nearby regulator, which is uncommon (27). However, a predicted NasR regulator is encoded immediately upstream of the nasFED operon.…”

Perspectives on the microbial carbon pump with special reference to microbial respiration and ecosystem efficiency in large estuarine systems

“…In certain coastal OMZs, there exists a cryptic S cycle, coupled to intensified denitrification and organic carbon mineralization processes (Thamdrup et al, 2010). Many heterotrophic microbes in general also assimilate nitrate and ammonium for biomass production (Cabello et al, 2004;Luque-Almagro et al, 2011;Zehr and Kudela, 2011). Thus, estuarine nutrients such as nitrate may be consumed mainly by heterotrophic microorganisms (especially by anaerobes) rather than being utilized by phytoplankton for carbon fixation and primary production.…”