Bart A. Smit

Flavour formation from amino acids by lactic acid bacteria: predictions from genome sequence analysis

Flavour development in dairy fermentations is the result of a series of chemical and biochemical processes during ripening. Starter lactic acid bacteria provide the enzymes involved in the formation of specific flavours. Amino acids, and in particular methionine, the aromatic and the branched-chain amino acids, are major precursors for volatile aroma compounds. The recent sequencing of complete genomes of several lactic acid bacteria (i.e. Lactococcus lactis, Lactobacillus plantarum, Streptococcus thermophilus) is beginning to provide insight into the full complement of proteins that may be involved in flavour-forming reactions, and hence the potential for formation of specific flavour compounds. Examples are given how bioinformatics tools can be used to search in genomes for essential components, such as proteinases, peptidases, aminotransferases, enzymes for biosynthesis of amino acids, and transport systems for peptides and amino acids.

Identification, Cloning, and Characterization of a Lactococcus lactis Branched-Chain α-Keto Acid Decarboxylase Involved in Flavor Formation

ABSTRACT The biochemical pathway for formation of branched-chain aldehydes, which are important flavor compounds derived from proteins in fermented dairy products, consists of a protease, peptidases, a transaminase, and a branched-chain α-keto acid decarboxylase (KdcA). The activity of the latter enzyme has been found only in a limited number of Lactococcus lactis strains. By using a random mutagenesis approach, the gene encoding KdcA in L. lactis B1157 was identified. The gene for this enzyme is highly homologous to the gene annotated ipd, which encodes a putative indole pyruvate decarboxylase, in L. lactis IL1403. Strain IL1403 does not produce KdcA, which could be explained by a 270-nucleotide deletion at the 3′ terminus of the ipd gene encoding a truncated nonfunctional decarboxylase. The kdcA gene was overexpressed in L. lactis for further characterization of the decarboxylase enzyme. Of all of the potential substrates tested, the highest activity was observed with branched-chain α-keto acids. Moreover, the enzyme activity was hardly affected by high salinity, and optimal activity was found at pH 6.3, indicating that the enzyme might be active under cheese ripening conditions.

Diversity of L-leucine catabolism in various microorganisms involved in dairy fermentations, and identification of the rate-controlling step in the formation of the potent flavour component 3-methylbutanal.

Various microorganisms, belonging to the genera Lactococcus, Lactobacillus, Streptococcus, Leuconostoc, Bifidobacterium, Propionibacterium, Brevibacterium, Corynebacterium and Arthrobacter, used in dairy fermentations such as cheese making, were analysed for their potential to convert leucine into flavour components, most notably 3-methylbutanal. A large variation between and within species was observed for various enzyme activities involved in the conversion pathway, e.g. transaminases, α-hydroxy acid dehydrogenase and α-keto acid decarboxylase. In particular, α-keto acid decarboxylase activity—leading to 3-methylbutanal—was found to be present in only two of the strains tested. It is proposed that this activity is rate-controlling in the conversion pathway leading to the flavour compound 3-methylbutanal.

Branched chain aldehydes: production and breakdown pathways and relevance for flavour in foods

Branched aldehydes, such as 2-methyl propanal and 2- and 3-methyl butanal, are important flavour compounds in many food products, both fermented and non-fermented (heat-treated) products. The production and degradation of these aldehydes from amino acids is described and reviewed extensively in literature. This paper reviews aspects influencing the formation of these aldehydes at the level of metabolic conversions, microbial and food composition. Special emphasis was on 3-methyl butanal and its presence in various food products. Knowledge gained about the generation pathways of these flavour compounds is essential for being able to control the formation of desired levels of these aldehydes.

Correlation of gene expression and protein production rate - a system wide study

BackgroundGrowth rate is a major determinant of intracellular function. However its effects can only be properly dissected with technically demanding chemostat cultivations in which it can be controlled. Recent work on Saccharomyces cerevisiae chemostat cultivations provided the first analysis on genome wide effects of growth rate. In this work we study the filamentous fungus Trichoderma reesei (Hypocrea jecorina) that is an industrial protein production host known for its exceptional protein secretion capability. Interestingly, it exhibits a low growth rate protein production phenotype.ResultsWe have used transcriptomics and proteomics to study the effect of growth rate and cell density on protein production in chemostat cultivations of T. reesei. Use of chemostat allowed control of growth rate and exact estimation of the extracellular specific protein production rate (SPPR). We find that major biosynthetic activities are all negatively correlated with SPPR. We also find that expression of many genes of secreted proteins and secondary metabolism, as well as various lineage specific, mostly unknown genes are positively correlated with SPPR. Finally, we enumerate possible regulators and regulatory mechanisms, arising from the data, for this response.ConclusionsBased on these results it appears that in low growth rate protein production energy is very efficiently used primarly for protein production. Also, we propose that flux through early glycolysis or the TCA cycle is a more fundamental determining factor than growth rate for low growth rate protein production and we propose a novel eukaryotic response to this i.e. the lineage specific response (LSR).

Transcriptional monitoring of steady state and effects of anaerobic phases in chemostat cultures of the filamentous fungus Trichoderma reesei

BackgroundChemostat cultures are commonly used in production of cellular material for systems-wide biological studies. We have used the novel TRAC (transcript analysis with aid of affinity capture) method to study expression stability of approximately 30 process relevant marker genes in chemostat cultures of the filamentous fungus Trichoderma reesei and its transformant expressing laccase from Melanocarpus albomyces. Transcriptional responses caused by transient oxygen deprivations and production of foreign protein were also studied in T. reesei by TRAC.ResultsIn cultures with good steady states, the expression of the marker genes varied less than 20% on average between sequential samples for at least 5 or 6 residence times. However, in a number of T. reesei cultures continuous flow did not result in a good steady state. Perturbations to the steady state were always evident at the transcriptional level, even when they were not measurable as changes in biomass or product concentrations. Both unintentional and intentional perturbations of the steady state demonstrated that a number of genes involved in growth, protein production and secretion are sensitive markers for culture disturbances. Exposure to anaerobic conditions caused strong responses at the level of gene expression, but surprisingly the cultures could regain their previous steady state quickly, even after 3 h O2 depletion. The main effect of producing M. albomyces laccase was down-regulation of the native cellulases compared with the host strain.ConclusionThis study demonstrates the usefulness of transcriptional analysis by TRAC in ensuring the quality of chemostat cultures prior to costly and laborious genome-wide analysis. In addition TRAC was shown to be an efficient tool in studying gene expression dynamics in transient conditions.

Differential effects of Lactobacillus acidophilus and Lactobacillus plantarum strains on cytokine induction in human peripheral blood mononuclear cells

Lactic acid bacterial strains have received interest for their immunomodulating activities and potential use in probiotic products. A wide variety of strain-dependent properties have been reported, but comparative studies at the species level are scarce. The objective of this study was to assess the immunomodulatory effect of Lactobacillus species on the cytokine profiles and proliferative response of human peripheral blood mononuclear cells (hPBMC), and in particular, on the comparison between the species Lactobacillus acidophilus and Lactobacillus plantarum. hPBMC from healthy donors were stimulated in the presence or absence of the lactic acid bacteria, and cytokine production, surface marker staining, proliferation and cell death were determined after 1 and 4 days of culture. All Lactobacillus strains tested were capable of inducing the production of interleukin (IL)-1beta, IL-10, interferon-gamma (IFN-gamma) and tumor necrosis factor-alpha (TNF-alpha). The bacterial strains did not differentially influence the amount of proliferating, viable, apoptotic and necrotic cells. Generally, L. plantarum showed a significantly higher induction capacity of IFN-gamma, IL-12 and TNF-alpha compared with L. acidophilus. We conclude that the variation in immunomodulatory effects between species is even larger than the variation between the strains of the same species. In addition, we demonstrate that L. plantarum strains are most potent in skewing the T-cell differentiation toward a putative Th1 response.

Development of a high throughput screening method to test flavour-forming capabilities of anaerobic micro-organisms.

Aim:  Development of a fast, automated and reliable screening method for screening of large collections of bacterial strains with minimal handling time.

Volatile sulphur compounds in morning breath of human volunteers

OBJECTIVE morning breath contains elevated concentrations of volatile sulphur components (VSCs). Therefore, morning breath is recognised as a surrogate target for interventions on breath quality. Nevertheless, factors influencing morning breath are poorly understood. Our aim was to evaluate concentrations of VSC at the time of awakening. METHODS a procedure was developed to collect breath samples at home. Intra- and inter-person variations were determined in two small studies based on measurements of hydrogen sulphide, methyl mercaptan and dimethyl sulphide in healthy volunteers. RESULTS highest levels of VSC were found directly after waking up, followed by a significant decline afterward. Considerable day-to-day variation was found, but could not be linked to dietary intake. A significantly higher concentration of H(2)S and CH(3)SH was observed in the group of female subjects compared to males. CONCLUSIONS when morning breath is used as a target for interventions, breath collected at the time of or shortly after waking up is preferred over breath collected later during the morning. Gender plays an important role in VSC levels, and should be taken into account.

Detecting novel genes with sparse arrays

Species-specific genes play an important role in defining the phenotype of an organism. However, current gene prediction methods can only efficiently find genes that share features such as sequence similarity or general sequence characteristics with previously known genes. Novel sequencing methods and tiling arrays can be used to find genes without prior information and they have demonstrated that novel genes can still be found from extensively studied model organisms. Unfortunately, these methods are expensive and thus are not easily applicable, e.g., to finding genes that are expressed only in very specific conditions. We demonstrate a method for finding novel genes with sparse arrays, applying it on the 33.9 Mb genome of the filamentous fungus Trichoderma reesei. Our computational method does not require normalisations between arrays and it takes into account the multiple-testing problem typical for analysis of microarray data. In contrast to tiling arrays, that use overlapping probes, only one 25 mer microarray oligonucleotide probe was used for every 100b. Thus, only relatively little space on a microarray slide was required to cover the intergenic regions of a genome. The analysis was done as a by-product of a conventional microarray experiment with no additional costs. We found at least 23 good candidates for novel transcripts that could code for proteins and all of which were expressed at high levels. Candidate genes were found to neighbour ire1 and cre1 and many other regulatory genes. Our simple, low-cost method can easily be applied to finding novel species-specific genes without prior knowledge of their sequence properties.