Negative regulation of DNA repair gene (uvrA) expression by ArcA/ArcB two-component system inEscherichia coli

UvrA expression of Lactococcus lactis NZ9000 improve multiple stresses tolerance and fermentation of lactic acid against salt stress

Lactococcus lactis is subjected to several stressful conditions during industrial fermentation including oxidation, heating and cooling, acid, high osmolarity/dehydration and starvation. DNA lesion is a major cause of genetic instability in L. lactis that usually occurs at a low frequency, but it is greatly enhanced by environmental stresses. DNA damages produced by these environmental stresses are thought to induce DNA double-strand breaks, leading to illegitimate recombination. Nucleotide excision repair (NER) protein UvrA suppresses multiple stresses-induced illegitimate recombination. UvrA protein can survive a coincident condition of environmental harsh conditions, multiple stress factors supposedly encountered in the host and inducing UvrA in L. lactis. In this study the expression of UvrA and growth performance and viability of control strain L. lactisVector and recombinant strain L. lactisUvrA under multiple stress conditions were determined. The recombinants strain had 30.70 and 52.67% higher growth performances when subjected to acidic and osmotic stresses conditions. In addition, the L. lactisUvrA strain showed 1.85-, 1.65-, and 2.40-fold higher biomass, lactate production, and lactate productivity, compared with the corresponding values for L. lactisVector strain during the osmotic stress. Results demonstrated NER system is involved in adaptation to various stress conditions and suggested that cells with a compromised UvrA as DNA repair system have an enhanced protection behavior in L. lactis NZ9000 against DNA damage.

The metabolic potential of Escherichia coli BL21 in defined and rich medium

BACKGROUND

The proteome reflects the available cellular machinery to deal with nutrients and environmental challenges. The most common E. coli strain BL21 growing in different, commonly employed media was evaluated using a detailed quantitative proteome analysis.

RESULTS

The presence of preformed biomass precursor molecules in rich media such as Luria Bertani supported rapid growth concomitant to acetate formation and apparently unbalanced abundances of central metabolic pathway enzymes, e.g. high levels of lower glycolytic pathway enzymes as well as pyruvate dehydrogenase, and low levels of TCA cycle and high levels of the acetate forming enzymes Pta and AckA. The proteome of cells growing exponentially in glucose-supplemented mineral salt medium was dominated by enzymes of amino acid synthesis pathways, contained more balanced abundances of central metabolic pathway enzymes, and a lower portion of ribosomal and other translational proteins. Entry into stationary phase led to a reconstruction of the bacterial proteome by increasing e.g. the portion of proteins required for scavenging rare nutrients and general cell protection. This proteomic reconstruction during entry into stationary phase was more noticeable in cells growing in rich medium as they have a greater reservoir of recyclable proteins from the translational machinery.

CONCLUSIONS

The proteomic comparison of cells growing exponentially in different media reflected the antagonistic and competitive regulation of central metabolic pathways through the global transcriptional regulators Cra, Crp, and ArcA. For example, the proteome of cells growing exponentially in rich medium was consistent with a dominating role of phosphorylated ArcA most likely a result from limitations in reoxidizing reduced quinones in the respiratory chain under these growth conditions. The proteomic alterations of exponentially growing cells into stationary phase cells were consistent with stringent-like and stationary phase responses and a dominating control through DksA-ppGpp and RpoS.

The bacterial response regulator ArcA uses a diverse binding site architecture to regulate carbon oxidation globally

Despite the importance of maintaining redox homeostasis for cellular viability, how cells control redox balance globally is poorly understood. Here we provide new mechanistic insight into how the balance between reduced and oxidized electron carriers is regulated at the level of gene expression by mapping the regulon of the response regulator ArcA from Escherichia coli, which responds to the quinone/quinol redox couple via its membrane-bound sensor kinase, ArcB. Our genome-wide analysis reveals that ArcA reprograms metabolism under anaerobic conditions such that carbon oxidation pathways that recycle redox carriers via respiration are transcriptionally repressed by ArcA. We propose that this strategy favors use of catabolic pathways that recycle redox carriers via fermentation akin to lactate production in mammalian cells. Unexpectedly, bioinformatic analysis of the sequences bound by ArcA in ChIP-seq revealed that most ArcA binding sites contain additional direct repeat elements beyond the two required for binding an ArcA dimer. DNase I footprinting assays suggest that non-canonical arrangements of cis-regulatory modules dictate both the length and concentration-sensitive occupancy of DNA sites. We propose that this plasticity in ArcA binding site architecture provides both an efficient means of encoding binding sites for ArcA, σ(70)-RNAP and perhaps other transcription factors within the same narrow sequence space and an effective mechanism for global control of carbon metabolism to maintain redox homeostasis.

Spontaneous mutagenesis associated with nucleotide excision repair in Escherichia coli

The vast majority of spontaneous mutations occurring in Escherichia coli are thought to be derived from spontaneous DNA lesions, which include oxidative base damage. Systems for removing intrinsic mutagens and repairing DNA lesions contribute to the suppression of spontaneous mutations. Nucleotide excision repair (NER) is a general DNA repair system that eliminates various kinds of lesions from DNA. We therefore predicted that NER might be involved in suppression of spontaneous mutations, and analyzed base substitutions occurring spontaneously within the rpoB gene in NER-proficient (wild-type), -deficient and -overproducing E. coli strains. Surprisingly, the mutation frequency was lower in NER-deficient strains, and higher in NER-overproducing strains, than in the NER-proficient strain. These results suggest, paradoxically, that NER contributes to the generation of spontaneous mutation rather than to its suppression under normal growth conditions, and that transcription-coupled repair also participates in this process. Using E. coli strains that carried an editing exonuclease-deficient polA mutation, we further obtained data suggesting that unnecessary NER might account for these findings, so that errors introduced during repair DNA synthesis by DNA polymerase I would result in unwanted base substitutions. The repair system itself may thus be an important generator of spontaneous mutation.

ArcA redox mutants as a source of reduced bioproducts

Escherichia coli and other facultative anaerobes can adapt their metabolism according to oxygen availability by means of aerobic and anaerobic respiration and fermentation. ArcAB is a two-component signal transduction system that controls, at the transcriptional level, the choice of energy generation pathway according to the intracellular redox state. High throughput studies on different redox regulator mutants, involving transcriptome analysis, RT-PCR and phenotypic arrays enabled the elucidation of a repertoire of operons coordinated by ArcA which extended beyond respiration control including, among others, those which code for survival, chromosome replication and degradation of fatty acids. Flux analysis by (13)C labeling provided new clues to the understanding of the distribution of metabolites mediated by ArcAB. The genetic manipulation of this regulator proved to be useful for the generation of reduced products of commercial value.

Signaling by the arc two-component system provides a link between the redox state of the quinone pool and gene expression

The Arc two-component system is a complex signal transduction system that plays a key role in regulating energy metabolism at the level of transcription in bacteria. This system comprises the ArcB protein, a tripartite membrane-associated sensor kinase, and the ArcA protein, a typical response regulator. Under anoxic growth conditions, ArcB autophosphorylates and transphosphorylates ArcA, which in turn represses or activates the expression of its target operons. Under aerobic conditions, ArcB acts as a phosphatase that catalyzes the dephosphorylation of ArcA-P and thereby releasing its transcriptional regulation. The events for Arc signaling, including signal reception and kinase regulation, signal transmission, amplification, as well as signal output and decay are discussed.