The arcABC gene cluster encoding the arginine deiminase pathway of Oenococcus oeni, and arginine induction of a CRP-like gene

Genomic Analysis of an Excellent Wine-Making Strain Oenococcus oeni SD-2a

Oenococcus oeni is an important microorganism in wine-making-related engineering, and it improves wine quality and stability through malolactic fermentation. Although the genomes of more than 200 O. oeni strains have been sequenced, only a few include completed genome maps. Here, the genome sequence of O. oeni SD-2a, isolated from Shandong, China, has been determined. It is a fully assembled genome sequence of this strain. The complete genome is 1,989,703 bp with a G+C content of 37.8% without a plasmid. The genome includes almost all the essential genes involved in central metabolic pathways and the stress genes reported in other O. oeni strains. Some natural competence-related genes, like comEA, comEC, comFA, comG operon, and comFC, suggest that O. oeni SD-2a may have natural transformation potential. A comparative genomics analysis revealed 730 gene clusters in O. oeni SD-2a homologous to those in four other lactic acid bacteria species (O. oeni PSU-1, O. oeni CRBO-11381, Lactiplantibacillus plantarum UNQLp11, and Pediococcus pentosaceus KCCM40703). A collinearity analysis showed poor collinearity between O. oeni SD-2a and

O. oeni PSU-1, indicating great differences in their evolutionary histories. The results provide general knowledge of O. oeni SD-2a and lay the foundation for specific gene function analyses.

Mechanisms of response to pH shock in microbial fermentation

The following review highlights pH shock, a novel environmental factor, as a tool for the improvement of fermentation production. The aim of this review is to introduce some recent original studies on the enhancement of microbial fermentation production by pH shock. Another purpose of this review is to improve the understanding of the processes that underlie physiological and genetic differences, which will facilitate future research on the improvement of fermentation production and reveal the associated molecular mechanisms. This understanding will simultaneously promote the application of this strategy to other microbial fermentation systems. Furthermore, improvement of the cellular tolerance of genetically engineered bacteria can also be a new field of research in the future to enhance fermentation production.

Heterologous Expression of Argininosuccinate Synthase From Oenococcus oeni Enhances the Acid Resistance of Lactobacillus plantarum

Oenococcus oeni can survive well in wine (an acid-stress environment) and dominate malolactic fermentation (MLF). To demonstrate a possible role of argininosuccinate synthase gene (argG) in the acid tolerance response of O. oeni, a related argG gene was inserted into a plasmid pMG36e and heterologously expressed in Lactobacillus plantarum SL09, a wine isolate belonging to a species of relevant importance in MLF. The expression levels of the argG gene in L. plantarum were analyzed by RT-qPCR, argininosuccinate synthase (ASS) activity and cell properties (amino acids, pH, H⁺-ATPase activity, and ATP levels) were determined at pH 3.7 in comparison with that at pH 6.3. Results showed that the recombinant strain L. plantarum SL09 (pMG36eargG) exhibited stronger growth performance compared with the control strain (without argG gene), and the expression levels of hsp1, cfa, atp, the citrate and malate metabolic genes were apparently increased under acid stress. In addition, the recombinant strain exhibited 11.0-, 2.0-, 1.9-fold higher ASS activity, H⁺-ATPase activity and intracellular ATP level, compared with the corresponding values for control strain during acid-stresses condition, which may take responsible for the acid tolerance enhancement of the recombinant strain. This is the first work report on heterologous expression of argG gene, and the results presented in this study will be beneficial for the research on acid stress response of O. oeni.

Urea production by yeasts other than Saccharomyces in food fermentation

Urea is an important intermediate in the synthesis of carcinogenic ethyl carbamate in various food fermentations. Identifying urea-producing microorganisms can help control or reduce ethyl carbamate production. Using Chinese liquor fermentation as a model system, we identified the yeasts responsible for urea production. Urea production was positively correlated to the yeast population (R = 0.523, P = 0.045), and using high-throughput sequencing, we identified 26 yeast species. Partial least squares regression and correlation analysis indicated that Wickerhamomyces anomalus was the most important yeast to produce urea (variable importance plot = 1.927; R = 0.719, P = 0.002). Besides, we found that in W. anomalus the CAR1 gene (responsible for urea production) was 67% identical to that of Saccharomyces cerevisiae. Wickerhamomyces anomalus produced more urea (910.0 μg L-1) than S. cerevisiae (300.1 μg L-1). Moreover, urea production increased to 1261.2 μg L-1 when the two yeasts were co-cultured in a simulated fermentation, where the transcription activity of the CAR1 gene increased by 140% in W. anomalus and decreased by 40% in S. cerevisiae. Our findings confirm that a yeast other than Saccharomyces, namely W. anomalus, contributes more to urea formation in a simulated sorghum fermentation. These findings provide the basis for strategies to control or reduce ethyl carbamate formation.

Participation of the arcRACME protein in self-activation of the arc operon located in the arginine catabolism mobile element in pandemic clone USA300

Staphylococcus aureus pandemic clone USA300 has, in addition to its constitutive arginine catabolism (arc) gene cluster, an arginine catabolism mobile element (ACME) carrying another such cluster, which gives this clone advantages in colonisation and infection. Gene arcR, which encodes an oxygen-sensitive transcriptional regulator, is inside ACME and downstream of the constitutive arc gene cluster, and this situation may have an impact on its activation. Different relative expression behaviours are proven here for arcR_ACME and the arc_ACME operon compared to the constitutive ones. We also show that the artificially expressed recombinant ArcR_ACME protein binds to the promoter region of the arc_ACME operon; this mechanism can be related to a positive feedback model, which may be responsible for increased anaerobic survival of the USA300 clone during infection-related processes.

Arginine deiminase pathway genes and arginine degradation variability in Oenococcus oeni strains

Trace amounts of the carcinogenic ethyl carbamate can appear in wine as a result of a reaction between ethanol and citrulline, which is produced from arginine degradation by some bacteria used in winemaking. In this study, arginine deiminase (ADI) pathway genes were evaluated in 44 Oenococcus oeni strains from wines originating from several locations in order to establish the relationship between the ability of a strain to degrade arginine and the presence of related genes. To detect the presence of arc genes of the ADI pathway in O. oeni, pairs of primers were designed to amplify arcA, arcB, arcC and arcD1 sequences. All strains contained these four genes. The same primers were used to confirm the organization of these genes in an arcABCD1 operon. Nevertheless, considerable variability in the ability to degrade arginine among these O. oeni strains was observed. Therefore, despite the presence of the arc genes in all strains, the expression patterns of individual genes must be strain dependent and influenced by the different wine conditions. Additionally, the presence of arc genes was also determined in the 57 sequenced strains of O. oeni available in GenBank, and the complete operon was found in 83% of strains derived from wine. The other strains were found to lack the arcB, arcC and arcD genes, but all contained sequences homologous to arcA, and some of them had also ADI activity.

Implications of new research and technologies for malolactic fermentation in wine

The initial conversion of grape must to wine is an alcoholic fermentation (AF) largely carried out by one or more strains of yeast, typically Saccharomyces cerevisiae. After the AF, a secondary or malolactic fermentation (MLF) which is carried out by lactic acid bacteria (LAB) is often undertaken. The MLF involves the bioconversion of malic acid to lactic acid and carbon dioxide. The ability to metabolise L-malic acid is strain specific, and both individual Oenococcus oeni strains and other LAB strains vary in their ability to efficiently carry out MLF. Aside from impacts on acidity, LAB can also metabolise other precursors present in wine during fermentation and, therefore, alter the chemical composition of the wine resulting in an increased complexity of wine aroma and flavour. Recent research has focused on three main areas: enzymatic changes during MLF, safety of the final product and mechanisms of stress resistance. This review summarises the latest research and technological advances in the rapidly evolving study of MLF and investigates the directions that future research may take.

A partial proteome reference map of the wine lactic acid bacterium Oenococcus oeni ATCC BAA-1163

Oenococcus oeni is the main lactic acid bacterium that carries out the malolactic fermentation in virtually all red wines and in some white and sparkling wines. Oenococcus oeni possesses an array of metabolic activities that can modify the taste and aromatic properties of wine. There is, therefore, industrial interest in the proteins involved in these metabolic pathways and related transport systems of this bacterium. In this work, we report the characterization of the O. oeni ATCC BAA-1163 proteome. Total and membrane protein preparations from O. oeni were standardized and analysed by two-dimensional gel electrophoresis. Using tandem mass spectrometry, we identified 224 different spots corresponding to 152 unique proteins, which have been classified by their putative function and subjected to bioinformatics analysis.

Effect of ethanol and low pH on citrulline and ornithine excretion and arc gene expression by strains of Lactobacillus brevis and Pediococcus pentosaceus

The accumulation of citrulline and ornithine in wine or beer as a result of the arginine catabolism of some lactic acid bacteria (LAB) species increases the risk of ethyl carbamate and putrescine formation, respectively. Several LAB species, which are found as spoilage bacteria in alcoholic beverages, have been reported to be arginine degrading. This study evaluates the effect of ethanol content and low pH on the excretion of citrulline and ornithine by two strains belonging to the potential contaminant species Lactobacillus brevis and Pediococcus pentosaceus. In the conditions that most affected cell viability, arginine consumption per cell increased noticeably, indicating that arginine utilization may be a stress responsive mechanism. L. brevis showed a higher accumulation of ornithine in the media than P. pentosaceus. In the presence of ethanol, a higher expression of the arcC gene was found in P. pentosaceus, which resulted in a lower excretion of citrulline and ornithine than in L. brevis. This suggests that L. brevis is more likely to produce these amino acids, which are precursors of ethyl carbamate and putrescine.

Wine features related to safety and consumer health: an integrated perspective

This review presents a global view of the current situation of the scientific knowledge about aspects of wine with possible repercussions (positive or negative) on consumer health and wine safety. The presence in wine of some potential harmful compounds such as phytosanitary products, trace metal compounds, sulfites, and some toxics of microbial origin, such as ochratoxin A, ethyl carbamate, and biogenic amines, is discussed. The different strategies and alternative methodologies that are being carried out to reduce or to avoid the presence of these substances in wines are also discussed. In recent years much work has focused on establishing the scientific explanations for the positive biological effects of some wine compounds. In this review, we also examine the latest knowledge regarding wine and health, focusing on two types of compounds that have been related to the positive effects of moderate wine consumption, such as phenolic compounds and bioactive peptides.

ADI pathway and histidine decarboxylation are reciprocally regulated in Lactobacillus hilgardii ISE 5211: proteomic evidence

Amine production by amino acid decarboxylation is a common feature that is used by lactic acid bacteria (LAB) to complement lactic fermentation, since it is coupled with a proton-extruding antiport system which leads to both metabolic energy production and the attenuation of intracellular acidity. Analogous roles are played in LAB by both malolactic fermentation (MLF) and the arginine deiminase (ADI) pathway. The present investigation was aimed at establishing reciprocal interactions between amino acid decarboxylation and the two above mentioned routes. The analyses were carried out on a Lactobacillus hilgardii strain (ISE 5211) that is able to decarboxylate histidine to histamine, which had previously been isolated from wine and whose complete genome is still unknown. The 2DE proteomic approach, followed by MALDI TOF-TOF and De Novo Sequencing, was used to study the protein expression levels. The experimental evidence has indicated that malate does not influence histidine decarboxylase (HDC) biosynthesis and that histidine does not affect the malolactic enzyme level. However, the expression of the ADI route enzymes, arginine deiminase and ornithine transcarbamylase, is down-regulated by histidine: this biosynthetic repression is more important (4-fold) in cultures that are not supplemented with arginine, but is also significant (2-fold) in an arginine supplemented medium that normally induces the ADI pathway. On the other hand, arginine partially represses HDC expression, but only when histidine and arginine are both present in the culture medium. This proteomic study has also pointed out a down-regulation exerted by histidine over sugar metabolism enzymes and a GroEL stress protein. These data, together with the reciprocal antagonism between arginine deimination and histidine decarboxylation, offer clue keys to the understanding of the accumulation of lactate, amine, ammonia and ethylcarbamate in wine, with consequent implications on different health risk controls.

Proteomics as a tool for studying energy metabolism in lactic acid bacteria

Lactic acid bacteria (LAB) are very ancient organisms that can't obtain metabolic energy by respiration without external heme supplementation. Since the gain in ATP from lactic fermentation is inadequate to support efficient growth, they developed alternative strategies for energy production. Three main energy generating routes are present in LAB: amino acid decarboxylation, malate decarboxylation and arginine deimination (ADI pathway). These routes, apart from supplying energy, also play a role in pH control. Lactic fermentation, which leads to lactic acid accumulation, causes a pH decrease that amino acid decarboxylations, originating basic amines, and the ADI pathway, giving rise to ammonia, may partially contrast. In the present mini-review, the reciprocal relationships among these metabolic pathways are considered, on the basis of proteomic results obtained from four different LAB strains, all of which possess the ADI pathway, but express different amino acid decarboxylases. The strains have been isolated and selected from different habitats and the role of some inducing molecules as well as of the growth phases is discussed. The overall results have revealed that LAB are complex biosystems able to set up a sophisticated metabolic regulation through a complex network of proteins that also include stress responses, as well as protease activation or inhibition.

Oenococcus oeni genome plasticity is associated with fitness

Oenococcus oeni strains are well-known for their considerable phenotypic variations in terms of tolerance to harsh wine conditions and malolactic activity. Genomic subtractive hybridization (SH) between two isolates with differing enological potentials was used to elucidate the genetic bases of this intraspecies diversity and identify novel genes involved in adaptation to wine. SH revealed 182 tester-specific fragments corresponding to 126 open reading frames (ORFs). A large proportion of the chromosome-related ORFs resembled genes involved in carbohydrate transport and metabolism, cell wall/membrane/envelope biogenesis, and replication, recombination, and repair. Six regions of genomic plasticity were identified, and their analysis suggested that both limited recombination and insertion/deletion events contributed to the vast genomic diversity observed in O. oeni. The association of selected sequences with adaptation to wine was further assessed by screening a large collection of strains using PCR. No sequences were found to be specific to highly performing (HP) strains alone. However, there was a statistically significant positive association between HP strains and the presence of eight gene sequences located on regions 2, 4, and 5. Gene expression patterns were significantly modified in HP strains, following exposure to one or more of the common stresses in wines. Regions 2 and 5 showed no traces of mobile elements and had normal GC content. In contrast, region 4 had the typical hallmarks of horizontal transfer, suggesting that the strategy of acquiring genes from other bacteria enhances the fitness of O. oeni strains.

Detection of arc genes related with the ethyl carbamate precursors in wine lactic acid bacteria

Trace amounts of the carcinogen ethyl carbamate can appear in wine by the reaction of ethanol with compounds such as citrulline and carbamyl phosphate, which are produced from arginine degradation by some wine lactic acid bacteria (LAB). In this work, the presence of arc genes for the arginine-deiminase pathway was studied in several strains of different species of LAB. Their ability to degrade arginine was also studied. To detect the presence of arc genes, degenerate primers were designed from the alignment of protein sequences in already sequenced LAB. The usefulness of these degenerate primers has been proven by sequencing some of the amplified PCR fragments and searching for homologies with published sequences of the same species and related ones. Correlation was found between the presence of genes and the ability to degrade arginine. Degrading strains included all heterofermentative lactobacilli, Oenococcus oeni , Pediococcus pentosaceus , and some strains of Leuconostoc mesenteroides and Lactobacillus plantarum .

Amino Acid Catabolic Pathways of Lactic Acid Bacteria

Lactic acid bacteria (LAB) constitute a diverse group of Gram positive obligately fermentative microorganisms which include both beneficial and pathogenic strains. LAB generally have complex nutritional requirements and therefore they are usually associated with nutrient-rich environments such as animal bodies, plants and foodstuffs. Amino acids represent an important resource for LAB and their utilization serves a number of physiological roles such as intracellular pH control, generation of metabolic energy or redox power, and resistance to stress. As a consequence, the regulation of amino acid catabolism involves a wide set of both general and specific regulators and shows significant differences among LAB. Moreover, due to their fermentative metabolism, LAB amino acid catabolic pathways in some cases differ significantly from those described in best studied prokaryotic model organisms such as Escherichia coli or Bacillus subtilis. Thus, LAB amino acid catabolism constitutes an interesting case for the study of metabolic pathways. Furthermore, LAB are involved in the production of a great variety of fermented products so that the products of amino acid catabolism are also relevant for the safety and the quality of fermented products.

Genetic structure and transcriptional analysis of the arginine deiminase (ADI) cluster inLactococcus lactisMG1363

In a recent proteomic analysis, we showed the overproduction of the ArcA and ArcB proteins in Lactococcus lactis MG1363 at low pH. The corresponding genes belong to the arcABD1C1C2TD2 cluster that encodes components of the arginine deiminase pathway. In this study, we characterized this cluster at the genetic level. Northern blot experiments showed the expression of at least seven transcripts, all induced by acidity. Tran script analysis using 5′RACE PCR (rapid amplification of cDNA ends polymerase chain reaction) in the arcB-arcD1intergenic region. In silico analysis identified nine stem-loop structures, all located in intergenic regions. Collectively, these data suggest a role for RNA processing and (or) premature termination in the differential expression of genes within the arcABD1C1C2TD2 cluster.Key words: lactic acid bacteria, acid stress, arginine catabolism.

Pathways and regulation of bacterial arginine metabolism and perspectives for obtaining arginine overproducing strains

L-arginine is produced by bacterial fermentation and is consumed in food flavoring and pharmaceutical industries. A better understanding of arginine metabolism in bacteria could be beneficial for a rational design of recombinant L-arginine producers by genetic engineering. This mini-review illustrated the current status of genes and enzymes for arginine metabolism, including biosynthetic pathways, catabolic pathways, uptake and excretion systems, and regulation. The linkage of polyamine and glutamate metabolism to the arginine network was also discussed, followed by a perspective view on how to construct arginine overproducing strains of bacteria with increasing biosynthesis and excretion and decreasing catabolism and uptake.

The arginine deiminase locus of Oenococcus oeni includes a putative arginyl-tRNA synthetase ArgS2 at its 3'-end

Oenococcus oeni is the most important lactic acid bacteria of the winemaking process involved in malolactic fermentation. Most O. oeni strains are able to catabolyze arginine via the arginine deiminase (ADI) pathway. The arcR, A, B, C, D1, and D2 cluster of O. oeni bacteria has been characterized. Here, we completed the ADI locus sequence. Downstream of arcD2 gene, we found an additional gene which encodes a putative arginyl-tRNA synthetase (argS2). It is not the same arginyl-tRNA synthetase which was sequenced in O. oeni MCW strain. Transcriptional analyses have shown that argS2 was induced by arginine. In addition, systematic polymerase chain reaction amplification of each arc gene and argS2 has provided a characteristic feature of the ADI locus within the O. oeni species: all genes of ADI locus are present or absent according to the strains.

Winemaking Biochemistry and Microbiology: Current Knowledge and Future Trends

The fermentation of grape must and the production of premium quality wines are a complex biochemical process that involves the interactions of enzymes from many different microbial species, but mainly yeasts and lactic acid bacteria. Yeasts are predominant in wine and carry out the alcoholic fermentation, while lactic acid bacteria are responsible for malolactic fermentation. Moreover, several optional winemaking techniques involve the use of technical enzyme preparations. Considerable progress has been made recently in understanding the biochemistry and interactions of enzymes during the winemaking process. In this study, some of these recent contributions in the biochemistry of winemaking are reviewed. This article intends to provide an updated overview (including works published until December, 2003) on the main biochemical and microbiological contributions of the different techniques that can be used in winemaking. As well as considering the transformations that take place in traditional winemaking, the production of special wines, such as sparkling wines, 'sur lie' wines, and biologically aged wines, are also studied.

Effect of nitrogen limitation and nature of the feed upon Oenococcus oeni metabolism and extracellular protein production

AIMS

The aim of the study was to characterize the effect of various nitrogen sources on Oenococcus oeni growth, carbon source utilization, extracellular protease activity and extracellular proteins. More generally, the goal is to understand how nitrogen-based additives might act to enhance malolactic fermentation in wine.

METHODS AND RESULTS

Five yeast extracts were used. As the amino acid and nitrogen analyses revealed, they were similar in global amino acid composition, except for arginine level. Nevertheless the ratio of amino acids between free/bound, and low/high molecular weight fractions were highly different. One of the yeast extracts led to a significant protease activity in the supernatant and to a poor final biomass of the IOB84.13 strain compared to the other ones. For the IOB84.13 strain specifically, arginine addition to the arginine poor yeast extract did not restore growth. 35S-methionine-labelled extracellular proteins were separated by SDS-PAGE. Signals were detected in all media early in the growth phase and were maintained during 48 h of culture.

CONCLUSIONS

A significant protease activity was detected for O. oeni supernatants during growth under nitrogen limitation but only for certain nitrogen sources. Moreover, the activity was strain dependent. Peptides (0.5-10 kDa) seemed to be more favourable for growth of wine bacteria than <0.5 kDa nitrogen sources. The extracellular protein signal patterns differed more greatly between the bacterial strains tested than between the nitrogen molecules in the medium.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first study extensively considering the role of the nitrogen source composition and level upon O. oeni growth and metabolism.

Expression analysis of putative arcA, arcB and arcC genes partially cloned from Lactobacillus plantarum isolated from wine

AIMS

The aim of this paper was to study if homofermentative strains (Lacobacillus plantarum) capable of malolactic fermentation in wine can degrade arginine via the ADI pathway.

METHODS AND RESULTS

Homofermentative lactic acid bacteria (LAB) isolated from a typical red wine were investigated for their ability to produce citrulline. Citrulline was formed suggesting that the arginine metabolism takes place via the arginine deiminase (ADI) pathway and not via the arginase/urease pathway. Ammonia was also detected with Nessler's reagent, and all the strains examined were able to produce ammonia. Identification of homofermentative LAB was performed using 16S ribosomal sequence analysis. The strains were further classified as belonging to L. plantarum species. Furthermore, the genes encoding for the three pathway enzymes (ADI, ornithine transcarbamylase, carbamate kinase) were partially cloned and gene expression was performed at two different pH values (3.6 and 4.5).

CONCLUSIONS

The results suggest that citrulline production in wine, could be performed by homofermentative LAB.

SIGNIFICANCE AND IMPACT OF THE STUDY

Homofermentative malolactic bacteria (L. plantarum) may degrade arginine through the ADI pathway.

Phylogeny of the bacterial superfamily of Crp-Fnr transcription regulators: exploiting the metabolic spectrum by controlling alternative gene programs

The Crp-Fnr regulators, named after the first two identified members, are DNA-binding proteins which predominantly function as positive transcription factors, though roles of repressors are also important. Among over 1200 proteins with an N-terminally located nucleotide-binding domain similar to the cyclic adenosine monophosphate (cAMP) receptor protein, the distinctive additional trait of the Crp-Fnr superfamily is a C-terminally located helix-turn-helix motif for DNA binding. From a curated database of 369 family members exhibiting both features, we provide a protein tree of Crp-Fnr proteins according to their phylogenetic relationships. This results in the assembly of the regulators ArcR, CooA, CprK, Crp, Dnr, FixK, Flp, Fnr, FnrN, MalR, NnrR, NtcA, PrfA, and YeiL and their homologs in distinct clusters. Lead members and representatives of these groups are described, placing emphasis on the less well-known regulators and target processes. Several more groups consist of sequence-derived proteins of unknown physiological roles; some of them are tight clusters of highly similar members. The Crp-Fnr regulators stand out in responding to a broad spectrum of intracellular and exogenous signals such as cAMP, anoxia, the redox state, oxidative and nitrosative stress, nitric oxide, carbon monoxide, 2-oxoglutarate, or temperature. To accomplish their roles, Crp-Fnr members have intrinsic sensory modules allowing the binding of allosteric effector molecules, or have prosthetic groups for the interaction with the signal. The regulatory adaptability and structural flexibility represented in the Crp-Fnr scaffold has led to the evolution of an important group of physiologically versatile transcription factors.

Surviving the acid test: responses of gram-positive bacteria to low pH

Gram-positive bacteria possess a myriad of acid resistance systems that can help them to overcome the challenge posed by different acidic environments. In this review the most common mechanisms are described: i.e., the use of proton pumps, the protection or repair of macromolecules, cell membrane changes, production of alkali, induction of pathways by transcriptional regulators, alteration of metabolism, and the role of cell density and cell signaling. We also discuss the responses of Listeria monocytogenes, Rhodococcus, Mycobacterium, Clostridium perfringens, Staphylococcus aureus, Bacillus cereus, oral streptococci, and lactic acid bacteria to acidic environments and outline ways in which this knowledge has been or may be used to either aid or prevent bacterial survival in low-pH environments.

Molecular characterization of Oenococcus oeni genes encoding proteins involved in arginine transport

AIMS

This work was carried out to complete the sequence of the arc cluster involved in arginine catabolism in Oenococcus oeni, and particularly to characterize the genes encoding proteins involved in arginine transport.

METHODS AND RESULTS

Using molecular cloning, two loci encoding proteins involved in the arginine-ornithine antiport were isolated. Their expression patterns were monitored by RT-PCR to study the influence of arginine on their transcription. Polycistronic mRNAs were detected. PCR performed directly on colonies with primer pairs specific of arc genes was used to discriminate strains able/unable to degrade arginine.

CONCLUSIONS

Oenococcus oeni contains two arcD loci encoding similar proteins. Their expression is not influenced by arginine and polycistronic messengers were detected. The inability to use arginine is due to a lack of genetic information encoding proteins of the arginine deiminase pathway.

SIGNIFICANCE AND IMPACT OF THE STUDY

The constitutive expression of arcD genes points to the positive role of arginine on O. oeni cell growth. The occasional presence of all the arc ABCD genes together in O. oeni strains might provide insights into the growth rate variability within this species.

The Product of arcR, the sixth gene of the arc operon of Lactobacillus sakei, is essential for expression of the arginine deiminase pathway

Lactobacillus sakei is a lactic acid bacterium commonly used as a starter culture for dry sausage production and can utilize arginine via the arginine deiminase pathway. The arcABCTD cluster of L. sakei has been characterized, and transcriptional studies have shown that its expression is subject to carbon catabolite repression and induction by arginine. Downstream of arcD an additional gene has been found; this gene, arcR, codes for a putative regulatory protein of the Crp/Fnr family. Transcriptional studies have shown that arcR is coordinately transcribed with the remaining arc genes, and therefore, these genes constitute the arcABCTDR operon. Northern analysis also showed a complex pattern of transcripts, suggesting that processing and partial termination may play a role in regulation of the expression of individual genes of the operon. Inactivation of arcR led to arrest of transcription of the operon, indicating that the ArcR protein is essential for expression of the arc genes. The availability of this mutant made it possible to study whether the ability to utilize arginine affects the growth of L. sakei in meat fermentations. Under our experimental conditions, expression of arginine deiminase does not confer an obvious advantage to L. sakei, since the wild type and an arcR mutant strain displayed similar dynamics of growth.

Arginine catabolism by sourdough lactic acid bacteria: purification and characterization of the arginine deiminase pathway enzymes from Lactobacillus sanfranciscensis CB1

The cytoplasmic extracts of 70 strains of the most frequently isolated sourdough lactic acid bacteria were screened initially for arginine deiminase (ADI), ornithine transcarbamoylase (OTC), and carbamate kinase (CK) activities, which comprise the ADI (or arginine dihydrolase) pathway. Only obligately heterofermentative strains such as Lactobacillus sanfranciscensis CB1; Lactobacillus brevis AM1, AM8, and 10A; Lactobacillus hilgardii 51B; and Lactobacillus fructivorans DD3 and DA106 showed all three enzyme activities. Lactobacillus plantarum B14 did not show CK activity. L. sanfranciscensis CB1 showed the highest activities, and the three enzymes were purified from this microorganism to homogeneity by several chromatographic steps. ADI, OTC, and CK had apparent molecular masses of ca. 46, 39, and 37 kDa, respectively, and the pIs were in the range of 5.07 to 5.2. The OTCs, CKs, and especially ADIs were well adapted to pH (acidic, pH 3.5 to 4.5) and temperature (30 to 37 degrees C) conditions which are usually found during sourdough fermentation. Internal peptide sequences of the three enzymes had the highest level of homology with ADI, OTC, and CK of Lactobacillus sakei. L. sanfranciscensis CB1 expressed the ADI pathway either on MAM broth containing 17 mM arginine or during sourdough fermentation with 1 to 43 mM added arginine. Two-dimensional electrophoresis showed that ADI, OTC, and CK were induced by factors of ca. 10, 4, and 2 in the whole-cell extract of cells grown in MAM broth containing 17 mM arginine compared to cells cultivated without arginine. Arginine catabolism in L. sanfranciscensis CB1 depended on the presence of a carbon source and arginine; glucose at up to ca. 54 mM did not exert an inhibitory effect, and the pH was not relevant for induction. The pH of sourdoughs fermented by L. sanfranciscensis CB1 was dependent on the amount of arginine added to the dough. A low supply of arginine (6 mM) during sourdough fermentation by L. sanfranciscensis CB1 enhanced cell growth, cell survival during storage at 7 degrees C, and tolerance to acid environmental stress and favored the production of ornithine, which is an important precursor of crust aroma compounds.

Gene structure, organization, expression, and potential regulatory mechanisms of arginine catabolism in Enterococcus faecalis

Although Enteroccus faecalis is the paradigm for biochemical studies on the arginine deiminase (ADI) pathway of fermentative arginine catabolism, little genetic information exists on this pathway in this organism. We fill this important gap by characterizing, in an 8,228-bp region cloned from a lambdagt11 genomic library of E. faecalis, a five-gene cluster forming a transcriptional unit (revealed by Northern blots and primer extension in E. faecalis) that corresponds to the ADI operon. Four additional genes in the opposite DNA strand and one in the same DNA strand are also identified. Studies on the protein products, including heterologous expression and/or sequence comparisons, allow us to ascertain or propose functions for all but 1 of the 10 genes. The ADI operon genes, arcABCRD, encode, respectively, ADI, ornithine transcarbamylase, carbamate kinase, a putative Crp/Fnr-type regulator (ArcR), and a putative ornithine-arginine antiporter (ArcD). Arginine induces the expression of arcABCRD, most likely by means of two homologous ArgR/AhrC-type regulators encoded by two genes, argR1 and argR2, that precede arcABCRD in each DNA strand and that are transcribed monocistronically, their transcription being influenced differentially by glucose and arginine. Potential ArgR1/ArgR2 (double and single) binding sequences are found in the promoter regions of arcA and of argR1/argR2 themselves. In addition, putative binding sequences for ArcR and for CcpA are found, respectively, in the argR1/argR2 and arcA promoter regions. Of the three other genes identified, two form a transcriptional unit and encode a putative metal-sensitive transcriptional regulator (ArsR) and a cysteine protease.