Physiological role and regulation of glutamate dehydrogenase inProchlorococcussp. strain MIT9313

Abstract

Glutamate dehydrogenase is an enzyme catalysing a reaction for ammonium assimilation, alternative to those performed by glutamine synthetase and glutamate synthase. In the genus Prochlorococcus, genomic studies have shown the presence of the gdhA gene (encoding glutamate dehydrogenase) in only four of the sequenced strains, including MIT9313. We studied the physiological regulation of glutamate dehydrogenase in this strain, by measuring the expression of gdhA, the intracellular concentration of the enzyme and its activity. Our goal was to clarify the physiological role of glutamate dehydrogenase, in order to understand why it has been selectively conserved in certain strains. Studies performed in cultures under nitrogen starvation, or with inhibitors of the nitrogen assimilation, suggest that the main role of glutamate dehydrogenase is not the assimilation of ammonium. Glutamate dehydrogenase activity and gdhA expression increased along the growth of cultures. Besides, we found a significant upregulation in gene expression when cultures were grown on glutamate as nitrogen source. We suggest that the main physiological role of glutamate dehydrogenase in Prochlorococcus MIT9313 is the utilization of glutamate to produce ammonium and 2-oxoglutarate, and amino acid recycling, thus enabling to use amino acids as nitrogen source. Therefore we propose that glutamate dehydrogenase is present in the genome of strains for whom the utilization of amino acids is most important.

Ecological Genomics of Marine Picocyanobacteria

“…It is, as yet, unclear whether GDH in Synechococcus and Prochlorococcus serves as glutamate dehydrogenase or partakes in the metabolism of amino acids. However, a recent study has (232). A major pathway for nitrogen recycling in the cyanobacterial cell is via the urea cycle, in which arginine enters a degradation route by which it generates urea and eventually cyanate.…”

Clade-Specific Quantitative Analysis of Photosynthetic Gene Expression in Prochlorococcus

“…As in previous works [ 28 ], Synechococcus cross-amplifications may occasionally occur, but it can be detected by using the differential Tm values of LL rbc L amplicons from both species. This improvement allows a fast and inexpensive method for the detection of cross-amplification that solves a major issue of the genetic similarity between these two genera, and simplifies the markers to just 6 pairs of primers instead of specific primers and/or probes for each strain [ 32 – 34 , 37 ]. This simplification is of great importance when using large sets of samples, as in our survey of samples from the Malaspina expedition.…”

“…Although genetic variability of Prochlorococcus has been extensively studied in the ocean, these studies were mainly based on the distinct sequences of the 16S and 23S rDNAs and the 16S/23S rRNA internal transcribed spacer (ITS) [ 7 , 20 , 22 , 28 , 30 , 31 ]. In contrast, analyses of functional gene expression are usually performed in laboratory conditions using pure cultures and specific probes for the target strains [ 32 – 37 ]. When functional genes have been studied in the field, the assessment has been restricted to a limited group of strains [ 38 , 39 ].…”

“…This gene encodes the RNA component of RNaseP, a ubiquitous enzyme required for tRNA 5’ end maturation in prokaryotes. It has been previously reported as a suitable reference gene for Prochlorococcus in qRT-PCR analyses [ 44 , 51 – 53 ], since its levels of mRNA remain stable at different conditions of irradiation, iron, phosphate, glucose, UV radiation, nitrogen, or light quality [ 32 – 37 , 43 , 52 , 54 , 55 ]. Aiming to integrate the high genetic variability of Prochlorococcus strains by a simple biomarker, we designed for each of the three tested genes, rnp B, rbc L and psb A, two separate sets of primers for HL and LL Prochlorococcus .…”

Short and direct science: Environmental Microbiology Reports

“…Futher insight into cyanobacteria is provided by the article by Rangel and colleagues (2009), in which the physiological role of glutamate dehydrogenase (GDH) is explored within the marine cyanobacteria Prochlorococcus – one of the main and most abundant primary producers on Earth (Coleman and Chisholm, 2007). The authors suggest that the main physiological role of GDH in Prochlorococcus MIT9313 is the utilization of glutamate to produce ammonium and 2‐oxoglutarate as part of the process of amino acid recycling, thus enabling the use of amino acids as source of nitrogen.…”