Nitrogen regulation of the xyl genes of Pseudomonas putida mt‐2 propagates into a significant effect of nitrate on m‐xylene mineralization in soil

The nitrogen species available in the growth medium are key factors determining expression of xyl genes for biodegradation of aromatic compounds by Pseudomonas putida. Nitrogen compounds are frequently amended to promote degradation at polluted sites, but it remains unknown how regulation observed in the test tube is propagated into actual catabolism of, e.g. m‐xylene in soil, the natural habitat of this bacterium. To address this issue, we have developed a test‐tube‐to‐soil model system that exposes the end‐effects of remediation practices influencing gene expression of P. putida mt‐2. We found that NO₃^? compared with NH₄⁺ had a stimulating effect on xyl gene expression in pure culture as well as in soil, and that this stimulation was translated into increased m‐xylene mineralization in soil. Furthermore, expression analysis of the nitrogen‐regulated genes amtB and gdhA allowed us to monitor nitrogen sensing status in both experimental systems. Hence, for nitrogen sources, regulatory patterns that emerge in soil reflect those observed in liquid cultures. The current study shows how distinct regulatory traits can lead to discrete environmental consequences; and it underpins that attempts to improve bioremediation by nitrogen amendment should integrate knowledge on their effects on growth and on catabolic gene regulation under natural conditions.     

Biosynthesis of secreted ribonucleases of <Emphasis Type="Italic">Bacillus intermedius</Emphasis> and <Emphasis Type="Italic">Bacillus circulans</Emphasis> under nitrogen starvation

The level of biosynthesis of secreted guanyl-specific ribonucleases (RNases) of Bacillus intermedius (binases) and Bacillus circulans (RNases Bci) by recombinant B. subtilis strains increases under nitrogen starvation. The promoter of the binase gene carries the sequences homologous to the recognition sites of the regulatory protein TnrA, which regulates gene expression under growth limitation by nitrogen. Using the B. subtilis strain defective in protein TnrA, it has been shown that the regulatory protein TnrA is involved in the regulation of expression of the binase gene and the gene of RNase Bci. The TnrA regulation of expression of the RNase Bci gene is indirect, probably by means of the regulatory protein PucR. Thus, it has been established that at least two regulatory mechanisms activate the expression of the genes encoding the secreted RNases of spore-forming bacteria: a system of proteins homologous to the B. subtilis PhoP-PhoR, and regulation by a protein similar to the B. subtilis TnrA regulatory protein.     

Effect of the regulation system of metabolic nitrogen exchange on biosynthesis of serine proteinases from <Emphasis Type="Italic">Bacillus intermedius</Emphasis>

The regulatory link between biosynthesis of Bacillus intermedius subtilisin-like serine proteinase and nitrogen metabolism in B. intermedius cells was determined. The level of the enzyme biosynthesis by the recombinant strain of Bacillus subtilis in the medium containing ammonium ions was three- to fivefold less than that in the medium with poorly utilized sodium nitrate. Accumulation of glutamyl endopeptidase in a culture liquid of this microorganism did not depend on the source of nitrogen present in the medium. During cultivation in the rich medium, the productivity of subtilisin-like proteinase in the recombinant B. subtilis strain carrying a mutation in the NrgB sensor protein was demonstrated to increase threefold compared to that of the control strain. In the minimal culture medium, mutation in the nrgB gene abolished the effect of a nitrogen source on the level of the subtilisin-like proteinase gene expression. At the same time, this mutation did not affect glutamyl endopeptidase biosynthesis. Thus, expression of the gene coding for subtilisin-like proteinase from B.intermedius is suggested to be positively regulated by the regulatory system of nitrogen metabolism.     

调控通路内基因表达的相关性分析

本研究从基因表达调控通路的角度分析了基因功能与基因表达之间的关系,利用7套酿酒酵母基因芯片表达谱数据和通路数据库（KEGG和CYGD）所提供的信息,应用我们研制的Genehub软件分析研究了同一基因表达调控通路内的基因在mRNA表达水平上的相关性,共涉及16条通路,495个基因。通过Pearson相关系数和Spearman相关系数两种相似性测度的分析,我们发现有94%（15条）的基因表达调控通路内的基因在大于等于4套的表达谱数据中是共表达的,以上结果从基因表达调控通路的角度,证实了基因功能与基因表达之间存在着一定的相关性。     

The response regulator RpaB binds the high light regulatory 1 sequence upstream of the high-light-inducible <Emphasis Type="Italic">hliB</Emphasis> gene from the cyanobacterium <Emphasis Type="Italic">Synechocystis</Emphasis> PCC 6803

Cyanobacteria, like other photosynthetic organisms, respond to the potentially damaging effects of high-intensity light by regulating the expression of a variety of stress-responsive genes through regulatory mechanisms that remain poorly understood. The high light regulatory 1 (HLR1) sequence can be found upstream of many genes regulated by high-light (HL) stress in cyanobacteria. In this study, we identify the factor that binds the HLR1 upstream of the HL-inducible hliB gene in the cyanobacterium Synechocystis PCC 6803 as the RpaB (Slr0947) response regulator.     

Regulatory Genes Controlling MPG1 Expression and Pathogenicity in the Rice Blast Fungus Magnaporthe grisea

MPG1, a pathogenicity gene of the rice blast fungus Magnaporthe grisea, is expressed during pathogenesis and in axenic culture during nitrogen or glucose limitation. We initiated a search for regulatory mutations that would impair nitrogen metabolism, MPG1 gene expression, and pathogenicity. First, we developed a pair of laboratory strains that were highly fertile and pathogenic toward barley. Using a combinatorial genetic screen, we identified mutants that failed to utilize a wide range of nitrogen sources (e.g., nitrate or amino acids) and then tested the effect of these mutations on pathogenicity. We identified five mutants and designated them Nr- (for nitrogen regulation defective). We show that two of these mutations define two genes, designated NPR1 and NPR2 (for nitrogen pathogenicity regulation), that are essential for pathogenicity and the utilization of many nitrogen sources. These genes are nonallelic to the major nitrogen regulatory gene in M. grisea and are required for expression of the pathogenicity gene MPG1. We propose that NPR1 and NPR2 are major regulators of pathogenicity in M. grisea and may be novel regulators of nitrogen metabolism in fungi.     

The Legionella pneumophila CpxRA two‐component regulatory system: new insights into CpxR's function as a dual regulator and its connection to the effectors regulatory network

Legionella pneumophila utilizes the Icm/Dot type‐IV secretion system to translocate approximately 300 effector proteins into host cells, and the CpxRA two‐component system (TCS) was previously shown to regulate the expression of several of these effectors. In this study, we expanded the pool of L. pneumophila CpxR‐regulated genes to 38, including 27 effector‐encoding genes. Our study demonstrates for the first time that the CpxR dual regulator has different requirements for activation and repression of target genes. These differences include the positioning of the CpxR regulatory element relative to the promoter element, and the effect of CpxR phosphate donors on the expression of CpxR target genes. In addition, unlike most response regulators, a mutant form of the L. pneumophila CpxR which cannot be phosphorylated was found to self‐interact, and to repress gene expression similarly to wild‐type CpxR, even though its ability to activate gene expression was reduced. Moreover, the CpxRA TCS was found to activate the expression of LetE which was found to function as a connector protein between the CpxRA TCS and the LetAS‐RsmYZ‐CsrA regulatory cascade. Our results show that CpxR plays a major role in L. pneumophila pathogenesis gene expression and functions as part of a regulatory network.