Curation and analysis of a saccharomyces cerevisiae genome-scale metabolic model for predicting production of sensory impact molecules under enological conditions
Scott, William T. ; Smid, Eddy J. ; Notebaart, Richard A. ; Block, David E. - \ 2020
Processes 8 (2020)9. - ISSN 2227-9717
Aroma - Flux balance analysis (FBA) - Genome-scalemetabolicmodels - Saccharomyces cerevisiae - Wine fermentation
One approach for elucidating strain-to-strain metabolic differences is the use of genome-scale metabolic models (GSMMs). To date GSMMs have not focused on the industrially important area of flavor production and, as such; do not cover all the pathways relevant to flavor formation in yeast. Moreover, current models for Saccharomyces cerevisiae generally focus on carbon-limited and/or aerobic systems, which is not pertinent to enological conditions. Here, we curate a GSMM (iWS902) to expand on the existing Ehrlich pathway and ester formation pathways central to aroma formation in industrial winemaking, in addition to the existing sulfur metabolism and medium-chain fatty acid (MCFA) pathways that also contribute to production of sensory impact molecules. After validating the model using experimental data, we predict key differences in metabolism for a strain (EC 1118) in two distinct growth conditions, including differences for aroma impact molecules such as acetic acid, tryptophol, and hydrogen sulfide. Additionally, we propose novel targets for metabolic engineering for aroma profile modifications employing flux variability analysis with the expanded GSMM. The model provides mechanistic insights into the key metabolic pathways underlying aroma formation during alcoholic fermentation and provides a potential framework to contribute to new strategies to optimize the aroma of wines.
Commonalities and Differences in the Transcriptional Response of the Model Fungus Saccharomyces cerevisiae to Different Commercial Graphene Oxide Materials
Laguna-Teno, Felix ; Suarez-Diez, Maria ; Tamayo-Ramos, Juan Antonio - \ 2020
Frontiers in Microbiology 11 (2020). - ISSN 1664-302X
biological response - chelating agent - commercial graphene oxide - differential expression - RNA isolation - Saccharomyces cerevisiae - transcriptomics
Graphene oxide has become a very appealing nanomaterial during the last years for many different applications, but its possible impact in different biological systems remains unclear. Here, an assessment to understand the toxicity of different commercial graphene oxide nanomaterials on the unicellular fungal model organism Saccharomyces cerevisiae was performed. For this task, an RNA purification protocol was optimized to avoid the high nucleic acid absorption capacity of graphene oxide. The developed protocol is based on a sorbitol gradient separation process for the isolation of adequate ribonucleic acid levels (in concentration and purity) from yeast cultures exposed to the carbon derived nanomaterial. To pinpoint potential toxicity mechanisms and pathways, the transcriptome of S. cerevisiae exposed to 160 mg L–1 of monolayer graphene oxide (GO) and graphene oxide nanocolloids (GOC) was studied and compared. Both graphene oxide products induced expression changes in a common group of genes (104), many of them related to iron homeostasis, starvation and stress response, amino acid metabolism and formate catabolism. Also, a high number of genes were only differentially expressed in either GO (236) or GOC (1077) exposures, indicating that different commercial products can induce specific changes in the physiological state of the fungus
Development of a low-alcoholic fermented beverage employing cashew apple juice and non-conventional yeasts
Gamero, Amparo ; Ren, Xiao ; Lamboni, Yendouban ; Jong, Catrienus de; Smid, Eddy J. ; Linnemann, Anita R. - \ 2019
Fermentation 5 (2019)3. - ISSN 2311-5637
Alcoholic beverages - Aroma profile - Cashew apple juice - Hanseniaspora guilliermondii - Non‐conventional yeasts - Saccharomyces cerevisiae - Torulaspora microellipsoides
Cashew apples are by‐products in the production of cashew nuts, which are mostly left to rot in the fields. Cashew apple juice (CAJ), a highly nutritious beverage, can be produced from them. It is rich in sugars and ascorbic acid, but its high polyphenol content makes it bitter and astringent, and therefore difficult to commercialize. The kingdom of fungi contains more than 2000 yeast species, of which only a few species have been studied in relation to their potential to produce aroma compounds. The aim of this research was to develop a new low‐alcoholic fermented beverage to valorize cashew apples. For this purpose, a screening was carried out employing non‐conventional yeast species and some species of the genus Saccharomyces for comparison, followed by a more detailed study with four selected strains cultured at different conditions. The production of volatile aroma compounds as a function of the presence of oxygen, temperature, and yeast species was investigated. The results showed that the more diverse aroma profiles appeared at 25 °C under anaerobic cultivation conditions, where Saccharomyces cerevisiae WUR 102 and Hanseniaspora guilliermondii CBS 2567 excelled in the synthesis of certain aroma compounds, such as β-phenylethanol and its acetate ester (rose aroma). Further studies are needed to test consumer acceptance of these new products.
Toward developing a yeast cell factory for the production of prenylated flavonoids
Levisson, Mark ; Araya-Cloutier, Carla ; Bruijn, Wouter J.C. De; Heide, Menno Van Der; Salvador López, José Manuel ; Daran, Jean Marc ; Vincken, Jean Paul ; Beekwilder, Jules - \ 2019
Journal of Agricultural and Food Chemistry 67 (2019)49. - ISSN 0021-8561 - p. 13478 - 13486.
8-prenylnaringenin - de novo - metabolic engineering - naringenin - prenylated flavonoids - Saccharomyces cerevisiae
Prenylated flavonoids possess a wide variety of biological activities, including estrogenic, antioxidant, antimicrobial, and anticancer activities. Hence, they have potential applications in food products, medicines, or supplements with health-promoting activities. However, the low abundance of prenylated flavonoids in nature is limiting their exploitation. Therefore, we investigated the prospect of producing prenylated flavonoids in the yeast Saccharomyces cerevisiae. As a proof of concept, we focused on the production of the potent phytoestrogen 8-prenylnaringenin. Introduction of the flavonoid prenyltransferase SfFPT from Sophora flavescens in naringenin-producing yeast strains resulted in de novo production of 8-prenylnaringenin. We generated several strains with increased production of the intermediate precursor naringenin, which finally resulted in a production of 0.12 mg L -1 (0.35 μM) 8-prenylnaringenin under shake flask conditions. A number of bottlenecks in prenylated flavonoid production were identified and are discussed.
Acetate-ester hydrolase activity for screening of the variation in acetate ester yield of Cyberlindnera fabianii, Pichia kudriavzevii and Saccharomyces cerevisiae
Rijswijck, Irma M.H. van; Kruis, Aleksander J. ; Wolkers – Rooijackers, Judith C.M. ; Abee, Tjakko ; Smid, Eddy J. - \ 2019
Food Science and Technology = Lebensmittel-Wissenschaft und Technologie 104 (2019). - ISSN 0023-6438 - p. 8 - 15.
Acetate esters - Alcohol acetyltransferase - Cyberlindnera fabianii - Pichia kudriavzevii - Saccharomyces cerevisiae
Esters constitute an important class of aroma compounds and contribute significantly to the aroma of yeast-fermented beverages. Ester formation is well studied in Saccharomyces cerevisiae, while production of aroma compounds by non-conventional yeasts has received little attention. The selection of such strains for co-culturing with S. cerevisiae offers opportunities for product innovations. Therefore, we performed a comparative analysis of the diversity in ester production by Cyberlindnera fabianii 65 (Cf65), Pichia kudriavzevii 129 (Pk129) and S. cerevisiae 131 (Sc131). For all three species distinct aroma profiles were identified, with Cf65 producing the highest amount of acetate esters. Since esters are formed from alcohols and acyl-CoA or acetyl-CoA, we analysed in vitro alcohol dehydrogenase and alcohol acetyl transferase activities in those three yeasts and found no correlation with ester formation. In contrast, a clear inverse correlation between the acetate-ester hydrolase activity and acetate ester yield was found for the three yeast species. Our study indicates that acetate-ester hydrolase activity plays a key role in determination of the final amount of acetate esters in fermentation broths.
CRISPR-Cas genome engineering of esterase activity in Saccharomyces cerevisiae steers aroma formation
Dank, Alexander ; Smid, Eddy J. ; Notebaart, Richard A. - \ 2018
BMC Research Notes 11 (2018)1. - ISSN 1756-0500 - 1 p.
Aroma - CRISRP-Cas9 - Esterase - Saccharomyces cerevisiae
OBJECTIVE: Saccharomyces cerevisiae is used worldwide for the production of ale-type beers. This yeast is responsible for the production of the characteristic fruity aroma compounds. Esters constitute an important group of aroma active secondary metabolites produced by S. cerevisiae. Previous work suggests that esterase activity, which results in ester degradation, may be the key factor determining the abundance of fruity aroma compounds. Here, we test this hypothesis by deletion of two S. cerevisiae esterases, IAH1 and TIP1, using CRISPR-Cas9 genome editing and by studying the effect of these deletions on esterase activity and extracellular ester pools.
RESULTS: Saccharomyces cerevisiae mutants were constructed lacking esterase IAH1 and/or TIP1 using CRISPR-Cas9 genome editing. Esterase activity using 5-(6)-carboxyfluorescein diacetate (cFDA) as substrate was found to be significantly lower for ΔIAH1 and ΔIAH1ΔTIP1 mutants compared to wild type (WT) activity (P < 0.05 and P < 0.001, respectively). As expected, we observed an increase in relative abundance of acetate and ethyl esters and an increase in ethyl esters in ΔIAH1 and ΔTIP1, respectively. Interestingly, the double gene disruption mutant ΔIAH1ΔTIP1 showed an aroma profile comparable to WT levels, suggesting the existence and activation of a complex regulatory mechanism to compensate multiple genomic alterations in aroma metabolism.
Engineering de novo anthocyanin production in Saccharomyces cerevisiae
Levisson, Mark ; Patinios, Constantinos ; Hein, Sascha ; Groot, Philip A. de; Daran, Jean M. ; Hall, Robert D. ; Martens, Stefan ; Beekwilder, Jules - \ 2018
Microbial Cell Factories 17 (2018)1. - ISSN 1475-2859
Anthocyanin - Flavonoids - Metabolic engineering - Natural products - Pelargonidin - Plant secondary metabolites - Saccharomyces cerevisiae
Background: Anthocyanins are polyphenolic pigments which provide pink to blue colours in fruits and flowers. There is an increasing demand for anthocyanins, as food colorants and as health-promoting substances. Plant production of anthocyanins is often seasonal and cannot always meet demand due to low productivity and the complexity of the plant extracts. Therefore, a system of on-demand supply is useful. While a number of other (simpler) plant polyphenols have been successfully produced in the yeast Saccharomyces cerevisiae, production of anthocyanins has not yet been reported. Results: Saccharomyces cerevisiae was engineered to produce pelargonidin 3-O-glucoside starting from glucose. Specific anthocyanin biosynthetic genes from Arabidopsis thaliana and Gerbera hybrida were introduced in a S. cerevisiae strain producing naringenin, the flavonoid precursor of anthocyanins. Upon culturing, pelargonidin and its 3-O-glucoside were detected inside the yeast cells, albeit at low concentrations. A number of related intermediates and side-products were much more abundant and were secreted into the culture medium. To optimize titers of pelargonidin 3-O-glucoside further, biosynthetic genes were stably integrated into the yeast genome, and formation of a major side-product, phloretic acid, was prevented by engineering the yeast chassis. Further engineering, by removing two glucosidases which are known to degrade pelargonidin 3-O-glucoside, did not result in higher yields of glycosylated pelargonidin. In aerated, pH controlled batch reactors, intracellular pelargonidin accumulation reached 0.01 μmol/gCDW, while kaempferol and dihydrokaempferol were effectively exported to reach extracellular concentration of 20 μM [5 mg/L] and 150 μM [44 mg/L], respectively. Conclusion: The results reported in this study demonstrate the proof-of-concept that S. cerevisiae is capable of de novo production of the anthocyanin pelargonidin 3-O-glucoside. Furthermore, while current conversion efficiencies are low, a number of clear bottlenecks have already been identified which, when overcome, have huge potential to enhance anthocyanin production efficiency. These results bode very well for the development of fermentation-based production systems for specific and individual anthocyanin molecules. Such systems have both great scientific value for identifying and characterising anthocyanin decorating enzymes as well as significant commercial potential for the production of, on-demand, pure bioactive compounds to be used in the food, health and even pharma industries.
Local fitness landscapes predict yeast evolutionary dynamics in directionally changing environments
Gorter, Florien A. ; Aarts, Mark G.M. ; Zwaan, Bas J. ; Visser, J.A.G.M. de - \ 2018
Genetics 208 (2018)1. - ISSN 0016-6731 - p. 307 - 322.
Experimental evolution - Fitness landscapes - Genotype-environment interaction - Predicting evolution - Saccharomyces cerevisiae
The fitness landscape is a concept that is widely used for understanding and predicting evolutionary adaptation. The topography of the fitness landscape depends critically on the environment, with potentially far-reaching consequences for evolution under changing conditions. However, few studies have assessed directly how empirical fitness landscapes change across conditions, or validated the predicted consequences of such change. We previously evolved replicate yeast populations in the presence of either gradually increasing, or constant high, concentrations of the heavy metals cadmium (Cd), nickel (Ni), and zinc (Zn), and analyzed their phenotypic and genomic changes. Here, we reconstructed the local fitness landscapes underlying adaptation to each metal by deleting all repeatedly mutated genes both by themselves and in combination. Fitness assays revealed that the height, and/or shape, of each local fitness landscape changed considerably across metal concentrations, with distinct qualitative differences between unconditionally (Cd) and conditionally toxic metals (Ni and Zn). This change in topography had particularly crucial consequences in the case of Ni, where a substantial part of the individual mutational fitness effects changed in sign across concentrations. Based on the Ni landscape analyses, we made several predictions about which mutations had been selected when during the evolution experiment. Deep sequencing of population samples from different time points generally confirmed these predictions, demonstrating the power of landscape reconstruction analyses for understanding and ultimately predicting evolutionary dynamics, even under complex scenarios of environmental change.
Effect of Microbial Interaction on Urea Metabolism in Chinese Liquor Fermentation
Wu, Qun ; Lin, Jianchun ; Cui, Kaixiang ; Du, Rubin ; Zhu, Yang ; Xu, Yan - \ 2017
Journal of Agricultural and Food Chemistry 65 (2017)50. - ISSN 0021-8561 - p. 11133 - 11139.
ethanol fermentation - ethyl carbamate - Lysinibacillus sphaericus - Saccharomyces cerevisiae - spontaneous food fermentation - urea
Urea is the primary precursor of the carcinogen ethyl carbamate in fermented foods. Understanding urea metabolism is important for controlling ethyl carbamate production. Using Chinese liquor as a model system, we used metatranscriptome analysis to investigate urea metabolism in spontaneous food fermentation processes. Saccharomyces cerevisiae was dominant in gene transcription for urea biosynthesis and degradation. Lysinibacillus sphaericus was dominant for urea degradation. S. cerevisiae degraded 18% and L. sphaericus degraded 13% of urea in their corresponding single cultures, whereas they degraded 56% of urea in coculture after 12 h. Compared to single cultures, transcription of CAR1, DAL2, and argA, which are related to urea biosynthesis, decreased by 51, 36, and 69% in coculture, respectively. Transcription of DUR1 and ureA, which are related to urea degradation, increased by 227 and 70%, respectively. Thus, coexistence of the two strains promoted degradation of urea via transcriptional regulation of genes related to urea metabolism.
Ethyl acetate production by the elusive alcohol acetyltransferase from yeast
Kruis, Alex ; Levisson, Mark ; Mars, Astrid E. ; Ploeg, Max van der; Garcés Daza, Fernando ; Ellena, Valeria ; Kengen, Servé W.M. ; Oost, John van der; Weusthuis, Ruud A. - \ 2017
Metabolic Engineering 41 (2017). - ISSN 1096-7176 - p. 92 - 101.
Alcohol acetyltransferase - Escherichia coli - Ethyl acetate - Saccharomyces cerevisiae - yeast - α/β hydrolase
Ethyl acetate is an industrially relevant ester that is currently produced exclusively through unsustainable processes. Many yeasts are able to produce ethyl acetate, but the main responsible enzyme has remained elusive, hampering the engineering of novel production strains. Here we describe the discovery of a new enzyme (Eat1) from the yeast Wickerhamomyces anomalus that resulted in high ethyl acetate production when expressed in Saccharomyces cerevisiae and Escherichia coli. Purified Eat1 showed alcohol acetyltransferase activity with ethanol and acetyl-CoA. Homologs of eat1 are responsible for most ethyl acetate synthesis in known ethyl acetate-producing yeasts, including S. cerevisiae, and are only distantly related to known alcohol acetyltransferases. Eat1 is therefore proposed to compose a novel alcohol acetyltransferase family within the α/β hydrolase superfamily. The discovery of this novel enzyme family is a crucial step towards the development of biobased ethyl acetate production and will also help in selecting improved S. cerevisiae brewing strains.
Analysis of the duodenal microbiotas of weaned piglet fed with epidermal growth factor-expressed Saccharomyces cerevisiae
Zhang, Zhongwei ; Cao, Lili ; Zhou, Yan ; Wang, Shujin ; Zhou, Lin - \ 2016
BMC Microbiology 16 (2016)1. - ISSN 1471-2180
Bacterial community - Epidermal growth factor - Full-length 16S rRNA - Saccharomyces cerevisiae - Weaned piglet
Background: The bacterial community of the small intestine is a key factor that has strong influence on the health of gastrointestinal tract (GIT) in mammals during and shortly after weaning. The aim of this study was to analyze the effects of the diets of supplemented with epidermal growth factor (EGF)-expressed Saccharomyces cerevisiae (S. cerevisiae) on the duodenal microbiotas of weaned piglets. Results: Revealed in this study, at day 7, 14 and 21, respectively, the compositional sequencing analysis of the 16S rRNA in the duodenum had no marked difference in microbial diversity from the phylum to species levels between the INVSc1(EV) and other recombinant strains encompassing INVSc1-EE(+), INVSc1-TE(-), and INVSc1-IE(+). Furthermore, the populations of potentially enterobacteria (e.g., Clostridium and Prevotella) and probiotic (e.g., Lactobacilli and Lactococcus) also remained unchanged among recombinant S. cerevisiae groups (P > 0.05). However, the compositional sequencing analysis of the 16S rRNA in the duodenum revealed significant difference in microbial diversity from phylum to species levels between the control group and recombinant S. cerevisiae groups. In terms of the control group (the lack of S. cerevisiae), these data confirmed that dietary exogenous S. cerevisiae had the feasibility to be used as a supplement for enhancing potentially probiotic (e.g., Lactobacilli and Lactococcus) (P < 0.01), and reducing potentially pathogenic bacteria (e.g., Clostridium and Prevotella) (P < 0.01). Conclusion: Herein, altered the microbiome effect was really S. cerevisiae, and then different forms of recombinant EGF, including T-EGF, EE-EGF and IE-EGF, did not appear to make a significant difference to the microbiome of weaned piglets.
Dynamics of adaptation in experimental yeast populations exposed to gradual and abrupt change in heavy metal concentration
Gorter, F.A. ; Aarts, M.M.G. ; Zwaan, B.J. ; Visser, Arjan de - \ 2016
American Naturalist 187 (2016)1. - ISSN 0003-0147 - p. 110 - 119.
Environmental change - Experimental evolution - Genotype-environment interaction - Heavy metals - Pleiotropy - Saccharomyces cerevisiae
Directional environmental change is a ubiquitous phe-nomenon that may have profound effects on all living organisms. However, it is unclear how different rates of such change affect the dynamics and outcome of evolution. We studied this question using experimental evolution of heavy metal tolerance in the baker’s yeast Saccharomyces cerevisiae. To this end, we grew replicate lines of yeast for 500 generations in the presence of (1) a constant high concentration of cadmium, nickel, or zinc or (2) a gradually increas-ing concentration of these metals. We found that gradual environ-mental change leads to a delay in fitness increase compared with abrupt change but not necessarily to a different fitness of evolution-ary endpoints. For the nonessential metal cadmium, this delay is due to reduced fitness differences between genotypes at low metal con-centrations, consistent with directional selection to minimize intra-cellular concentrations of this metal. In contrast, for the essential metals nickel and zinc, different genotypes are selected at different concentrations, consistent with stabilizing selection to maintain con-stant intracellular concentrations of these metals. These findings in-dicate diverse fitness consequences of evolved tolerance mechanisms for essential and nonessential metals and imply that the rate of en-vironmental change and the nature of the stressor are crucial deter-minants of evolutionary dynamics.
Evaluation of the bioactive properties of avenanthramide analogs produced in recombinant yeast
Moglia, Andrea ; Goitre, Luca ; Gianoglio, Silvia ; Beekwilder, Jules - \ 2015
BioFactors 41 (2015)1. - ISSN 0951-6433 - p. 15 - 27.
Antioxidants - Avenanthramides - Biofactors - Cerebral cavernous malformation - Metabolic engineering - Phenolic compounds - Plant secondary metabolites - Saccharomyces cerevisiae
Saccharomyces cerevisiae has been proven to be a valuable tool for the expression of plant metabolic pathways. By engineering a S. cerevisiae strain with two plant genes (4cl-2 from tobacco and hct from globe artichoke) we previously set up a system for the production of two novel phenolic compounds, N-(E)-p-coumaroyl-3-hydroxyanthranilic acid (Yeast avenanthramide I, Yav I) and N-(E)-caffeoyl-3-hydroxyanthranilic acid (Yeast avenanthramide II, Yav II). These compounds have a structural similarity with a class of bioactive oat compounds called avenanthramides. By developing a fermentation process for the engineered S. cerevisiae strain, we obtained a high-yield production of Yav I and Yav II. To examine the biological relevance of these compounds, we tested their potential antioxidant and antiproliferative properties upon treatment of widely used cell models, including immortalized mouse embryonic fibroblast cell lines and HeLa cancer cells. The outcomes of our experiments showed that both Yav I and Yav II enter the cell and trigger a significant up-regulation of master regulators of cell antioxidant responses, including the major antioxidant protein SOD2 and its transcriptional regulator FoxO1 as well as the down-regulation of Cyclin D1. Intriguingly, these effects were also demonstrated in cellular models of the human genetic disease Cerebral Cavernous Malformation, suggesting that the novel phenolic compounds Yav I and Yav II are endowed with bioactive properties relevant to biomedical applications. Taken together, our data demonstrate the feasibility of biotechnological production of yeast avenanthramides and underline a biologically relevant antioxidant activity of these molecules.
Use of genome-scale metabolic models in evolutionary systems biology
Papp, Balázs ; Szappanos, Balázs ; Notebaart, Richard A. - \ 2011
In: Yeast Systems Biology / Castrillo, Juan I., Oliver, Stephen G., Humana Press (Methods in Molecular Biology ) - ISBN 9781617791727 - p. 483 - 497.
constraint-based modeling - fitness landscape - Flux balance analysis (FBA) - gene essentiality - genetic interaction - genome evolution - metabolic network - Saccharomyces cerevisiae
One of the major aims of the nascent field of evolutionary systems biology is to test evolutionary hypotheses that are not only realistic from a population genetic point of view but also detailed in terms of molecular biology mechanisms. By providing a mapping between genotype and phenotype for hundreds of genes, genome-scale systems biology models of metabolic networks have already provided valuable insights into the evolution of metabolic gene contents and phenotypes of yeast and other microbial species. Here we review the recent use of these computational models to predict the fitness effect of mutations, genetic interactions, evolutionary outcomes, and to decipher the mechanisms of mutational robustness. While these studies have demonstrated that even simplified models of biochemical reaction networks can be highly informative for evolutionary analyses, they have also revealed the weakness of this modeling framework to quantitatively predict mutational effects, a challenge that needs to be addressed for future progress in evolutionary systems biology.
Method for the production of hydroxylated collagen-like compounds using prolyl hydroxylase from Hansenula polymorpha
Bruin, E.C. de; Werten, M.W.T. ; Wolf, F.A. de - \ 2002
Octrooinummer: WO0204615, gepubliceerd: 2002-01-17.
Collagens, preparation - Proteins - Hydroxylation - Microorganism - Glyoproteins - Gelatins, processes - Cryptococcus curvatus - Fungi - Kluyveromyces lactis - Komagataella pastoris - Pichia angusta - Saccharomyces cerevisiae - Cryptococcus curvatus - Kluyveromyces lactis - Komagataella pastoris - Pichia angusta - Saccharomyces cerevisiae
The present invention relates to a method for the production of collagen-like compounds containing hydroxylated proline residues. Of specific interest is the production of recombinant collagen-like compounds in which hydroxylation of proline residues is achieved by a prolyl hydroxylase from a fungus, preferably a yeast, in particular Hansenula polymorpha. Also the invention concerns a method for controlling the hydroxylation of proline residues by such a prolyl hydroxylase characterised by the addition of collagen-like oligopeptides, such as gelatine hydrolysate, in particular gelatone or peptone.