Acid Stress Response Research Articles

CDNA-AFLP analysis of salicylic acid- and calcium chloride-induced transcript derived fragments under drought in tomato (Solanum lycopersicum)

Drought seriously threatens tomato production worldwide. Despite much research on exogenous salicylic acid (SA) and Ca2+ improving plant resistance to biotic and abiotic stress, the molecular mechanisms of exogenous SA- and Ca2+-mediated drought resistance response in tomato remain unclear. In this study, we analyzed SA- and Ca2+ -induced differentially expressed transcripts under drought in tomato plants using cDNA-amplified fragment length polymorphism (cDNA-AFLP). In total, 34 transcript derived fragments (TDFs) were differentially expressed. The functions identified through NCBI BLAST alignment mainly involved signal transduction, amino acid metabolism, transcription factors, transfer transport and stress response. The quantitative real-time polymerase chain reaction results of 12 TDFs associated with drought response were consistent with the patterns of changes observed with cDNA-AFLP analysis. These differentially expressed transcripts may be used for functional verification, transgenic research and breeding of drought-resistant tomato varieties.

Transcriptomic insights into the molecular aspects of salt stress responses in Kandelia candel roots

The mangrove plant Kandelia candel is a type of woody halophyte that grows in tropical and subtropical ocean intertidal zones and exhibits a high salt tolerance. In this study, 61,970 unigenes were obtained from the roots of 60-day-old K. candel seedlings treated with 0 (control), 200, 400, and 600 mM NaCl for 3 days with an N50 of 1510 bp. Moreover, 454, 311, and 2663 genes were differentially expressed under 200, 400, and 600 mM NaCl treatments, respectively. These differentially expressed genes were primarily involved in plant hormone signal transduction, carbohydrate and energy metabolism, amino acid metabolism, stress response, and defense. The levels of 12 important differentially expressed genes were confirmed by qRT-PCR, showing that the changing trend was generally consistent with the results of the transcriptomic analysis. In addition, physiological parameters involved in energy metabolism, amino acid metabolism, and the reactive oxygen species scavenging process were significantly increased under salt stress treatment, and the trend was consistent with the results of transcription and qRT-PCR. This study indicated that K. candel roots could tolerate high salt stress by enhancing ethylene signal transduction, maintaining a stable energy supply, increasing antioxidant capacity. Specially, we found that accumulation of ?-aminobutyric acid and glutamate, but not proline, might play an important role in salt tolerance in the roots of K. candel.

Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli.

Response to acid stress is critical for Escherichia coli to successfully complete its life-cycle by passing through the stomach to colonize the digestive tract. To develop a fundamental understanding of this response, we established a molecular mechanistic description of acid stress mitigation responses in E. coli and integrated them with a genome-scale model of its metabolism and macromolecular expression (ME-model). We considered three known mechanisms of acid stress mitigation: 1) change in membrane lipid fatty acid composition, 2) change in periplasmic protein stability over external pH and periplasmic chaperone protection mechanisms, and 3) change in the activities of membrane proteins. After integrating these mechanisms into an established ME-model, we could simulate their responses in the context of other cellular processes. We validated these simulations using RNA sequencing data obtained from five E. coli strains grown under external pH ranging from 5.5 to 7.0. We found: i) that for the differentially expressed genes accounted for in the ME-model, 80% of the upregulated genes were correctly predicted by the ME-model, and ii) that these genes are mainly involved in translation processes (45% of genes), membrane proteins and related processes (18% of genes), amino acid metabolism (12% of genes), and cofactor and prosthetic group biosynthesis (8% of genes). We also demonstrated several intervention strategies on acid tolerance that can be simulated by the ME-model. We thus established a quantitative framework that describes, on a genome-scale, the acid stress mitigation response of E. coli that has both scientific and practical uses.

A label-free shotgun proteomics analysis of macadamia nut.

In this study, we present a systematic proteomic overview of macadamia nut using a label-free shotgun proteomic approach. We identified 947 proteins in 723 clusters and gene ontology analysis revealed proteins across 46 functional categories including carbohydrate metabolism (10%), protein metabolic processes (5%), amino acid metabolism (4%), transport (4%), stress response (3%), lipid metabolism (3%), protein folding (3%) and defense response (1.4%). The defense response proteins accounted for 24% of the total peptide abundance. The vicilin-like macadamia antimicrobial peptides 2-3 (MiAMP2) was the most abundant protein, followed by glyceraldehyde-3-phosphate dehydrogenase 3, 11S legumin-like protein, 2-phospho-D-glycerate hydrolase and heat shock 70kDa protein among others. The cascading of amino acid and carbohydrate metabolic pathways in macadamia nut were constructed against reference maps from KEGG and proposed for the first time. Results were also indicative of useful protein candidates with possible allergenic potential and cross-reactivity in macadamia nut. The in-silico analysis revealed homology and linear epitope similarities to known allergens such as conglutin β allergen from lupin, Jug r2 vicilin allergens from walnut, Ara h3 11S globulin from peanut, small rubber particle protein Hev b3, hevein, enolase 2, HSP 70kDa Cla h4, Der f28 allergen, and methylglyoxalases. Label-free shotgun proteomics reveal valuable insights into the genetic and biological makeup of macadamia nut proteome and provide guidance on protein candidates with allergenic potential for further immunological investigation. Data are available via ProteomeXchange with identifier PXD015364.

Parallel Bud Mutation Sequencing Reveals that Fruit Sugar and Acid Metabolism Potentially Influence Stress in Malus.

Apple sugar and acid are the most important traits of apple fruit. Bud sport cultivars can provide abundant research materials for functional gene studies in apple. In this study, using bud sport materials with a rather different sugar and acid flavor, i.e., “Jonathan” and “Sweet Jonathan”, we profiled the whole genome variations and transcriptional regulatory network during fruit developmental stages using whole genome sequencing and RNA-sequencing. Variation analysis identified 4,198,955 SNPs, 319,494 InDels, and 32,434 SVs between the two cultivars. In total, 4313 differentially expressed genes among all of the d 44,399 genes expressed were identified between the two cultivars during fruit development, and functional analysis revealed stress response and signal transduction related genes were enriched. Using 24,047 genes with a more variable expression value, we constructed 28 co-expression modules by weighted correlation network analysis. Deciphering of 14 co-expression modules associated with sugar or acid accumulation during fruit development revealed the hub genes associated with sugar and acid metabolism, e.g., MdDSP4, MdINVE, and MdSTP7. Furthermore, exploration of the intra network of the co-expression module indicated the close relationship between sugar and acid metabolism or sugar and stress. Motif-based sequence analysis of the 17 differentially expressed ATP-binding cassette transporter genes and Yeast one-hybrid assay identified and confirmed a transcription factor, MdBPC6, regulating the ATP-binding cassette (ABC) transporter genes and potentially participating in the apple fruit development or stress response. Collectively, all of the results demonstrated the use of parallel bud mutation sequencing and identified hub genes, and inferred regulatory relationships providing new information about apple fruit sugar and acid accumulation or stress response.

Comparative transcriptome analysis reveals positive effects of arbuscular mycorrhizal fungi inoculation on photosynthesis and high-pH tolerance in blueberry seedlings

Our results based on transcriptome data and physiological alterations give an account for enhancing high-pH tolerance in blueberry seedlings with AMF inoculation. To understand the responses occurring in leaves of arbuscular mycorrhizal fungi (AMF)-inoculated plants under high-pH stress, we combined physiological analyses with leaf transcriptome profiles of AMF-inoculated and non-inoculated blueberry (Vaccinium corymbosum) cultivar “O’Neal” under optimal-pH (pH 4.2) and high-pH (pH 6.2) conditions. Comparative transcriptome analysis revealed 250 differentially expressed genes (DEGs) in AMF-inoculated plants when compared with non-inoculated plants under high-pH stress. These DEGs were involved in 37 metabolic pathways, such as photosynthesis, hormone metabolism, carbohydrate metabolism, amino acid metabolism, stress response, signal transduction, and antioxidation. Physiological analyses revealed that AMF-inoculated plants presented lower respiration and higher photosynthesis efficiency under high-pH stress, along with accumulation of photosystem II reaction center PsbP family protein, enhancement of amino acids content, and stronger secondary metabolites biosynthesis ability, when compared with non-inoculated plants. These results provide new insights into a probable mechanism of protection of photosynthesis and enhancement of high-pH tolerance in blueberry seedlings with AMF inoculation.

Salmonella adapts to plants and their environment during colonization of tomatoes.

Humans and animals are considered typical hosts for Salmonella, however, also plants can be colonized. Tomatoes were linked to salmonellosis outbreaks already on several occasions. The aim of this study was, therefore, to establish a comprehensive view on the interaction between Salmonella enterica and tomatoes, and to test the hypothesis that colonization of plants is an interactive process. We assessed the persistence of Salmonella in agricultural soil, the colonization pattern in and on tomatoes, as well as the reciprocal responses of tomatoes to different Salmonella strains and Salmonella to root exudates and tomato-related media. This study revealed that Salmonella can persist in the soil and inside the tomato plant. Additionally, we show that Salmonella strains have particular colonization pattern, although the persistence inside the plant differs between the tested strains. Furthermore, the transcriptome response of tomato showed an up-regulation of several defense-related genes. Salmonella transcriptome analysis in response to the plant-based media showed differentially regulated genes related to amino acid and fatty acid synthesis and stress response, while the response to root exudates revealed regulation of the glyoxylate cycle. Our results indicate that both organisms actively engage in the interaction and that Salmonella adapts to the plant environment.

Adaptational changes in physiological and transcriptional responses of Bifidobacterium longum involved in acid stress resistance after successive batch cultures

Bifidobacterium inhabiting the human and animal intestinal tract is known for its health-promoting effect. Tolerance to acid stress is crucial for bifidobacteria to survive and then exert their beneficial effects in the gut. A long-term adaptation in successive batch cultures was used as evolutionary engineering strategy to improve acid stress tolerance in an industrial probiotic strain, B. longum JDM301. Its derivative, JDM301AR showed higher resistance to several stress conditions, including acid stress than the parental strain, JDM301. To better understand bifidobacterial acid stress response, the changes of fatty acid (FA) in cell membrane of these two strains were determined. A shift in the production of FA in cell membrane, characterized by increased C14:0 was found, when JDM301AR was exposed to low-pH environment. It was implied that the increased production of C14:0 is associated with the acquisition of acid-tolerant phenotype for JDM301AR. High-throughput RNA-sequencing was performed to analyze the changes of gene expression profile after acid-exposure. The transcriptional profiles of JDM301AR and JDM301 under normal condition and acid stress were compared to reveal the different acid response between them. A total of 5 genes involved in FA metabolism were upregulated and no downregulated genes were found in response to acid stress in JDM301AR. The up-regulated BLJ_0565 and BLJ_1105 may play important roles in the modification of membrane FA composition of JDM301AR after acid exposure. Overall, these results suggested that successive batch cultures induced the acid stress tolerance of B. longum involved in transcriptional and physiological responses, including modification of cell wall and cell membrane, metabolism of amino acid and neutralization of internal pH by strengthening NH3 production and transport.

Bacterial Cyclopropane Fatty Acid Synthase mRNA Is Targeted by Activating and Repressing Small RNAs.

Altering membrane protein and lipid composition is an important strategy for maintaining membrane integrity during environmental stress. Many bacterial small RNAs (sRNAs) control membrane protein production, but sRNA-mediated regulation of membrane fatty acid composition is less well understood. The sRNA RydC was previously shown to stabilize cfa (cyclopropane fatty acid synthase) mRNA, resulting in higher levels of cyclopropane fatty acids in the cell membrane. Here, we report that additional sRNAs, ArrS and CpxQ, also directly regulate cfa posttranscriptionally. RydC and ArrS act through masking an RNase E cleavage site in the cfa mRNA 5' untranslated region (UTR), and both sRNAs posttranscriptionally activate cfa In contrast, CpxQ binds to a different site in the cfa mRNA 5' UTR and represses cfa expression. Alteration of membrane lipid composition is a key mechanism for bacteria to survive low-pH environments, and we show that cfa translation increases in an sRNA-dependent manner when cells are subjected to mild acid stress. This work suggests an important role for sRNAs in the acid stress response through regulation of cfa mRNA.IMPORTANCE Small RNAs (sRNAs) in bacteria are abundant and play important roles in posttranscriptional regulation of gene expression, particularly under stress conditions. Some mRNAs are targets for regulation by multiple sRNAs, each responding to different environmental signals. Uncovering the regulatory mechanisms governing sRNA-mRNA interactions and the relevant conditions for these interactions is an ongoing challenge. In this study, we discovered that multiple sRNAs control membrane lipid composition by regulating stability of a single mRNA target. The sRNA-dependent regulation occurred in response to changing pH and was important for cell viability under acid stress conditions. This work reveals yet another aspect of bacterial physiology controlled at the posttranscriptional level by sRNA regulators.

Proteomic Analysis of Rhizobium favelukesii LPU83 in Response to Acid Stress.

Acid soils constitute a severe problem for leguminous crops mainly through a disturbance in rhizobium-legume interactions. Rhizobium favelukesii-an acid-tolerant rhizobium able to nodulate alfalfa-is highly competitive for nodule occupation under acid conditions but inefficient for biologic nitrogen fixation. In this work, we obtained a general description of the acid-stress response of R. favelukesii LPU83 by means of proteomics by comparing the total proteome profiles in the presence or absence of acid stress by nanoflow ultrahigh-performance liquid chromatography coupled to mass spectrometry. Thus, a total of 336 proteins were identified with a significant differential expression, 136 of which species were significantly overexpressed and 200 underexpressed in acidity. An in silico functional characterization with those respective proteins revealed a complex and pleiotropic response by these rhizobia involving components of oxidative phosphorylation, glutamate metabolism, and peptidoglycan biosynthesis, among other pathways. Furthermore, a lower permeability was evidenced in the acid-stressed cells along with several overexpressed proteins related to γ-aminobutyric acid metabolism, such as the gene product of livK, which gene was mutated. This mutant exhibited an acid-sensitive phenotype in agreement with the proteomics results. We conclude that both the γ-aminobutyric acid metabolism and a modified cellular envelope could be relevant to acid tolerance in R. favelukesii.

Proteomic characterization of MPK4 signaling network and putative substrates.

Combining genetic engineering of MPK4 activity and quantitative proteomics, we established an in planta system that enables rapid study of MPK4 signaling networks and potential substrate proteins. Mitogen activated protein kinase 4 (MPK4) is a multifunctional kinase that regulates various signaling events in plant defense, growth, light response and cytokinesis. The question of how a single protein modulates many distinct processes has spurred extensive research into the physiological outcomes resulting from genetic perturbation of MPK4. However, the mechanism by which MPK4 functions is still poorly understood due to limited data on the MPK4 networks including substrate proteins and downstream pathways. Here we introduce an experimental system that combines genetic engineering of kinase activity and quantitative proteomics to rapidly study the signaling networks of MPK4. First, we transiently expressed a constitutively active (MPK4CA) and an inactive (MPK4IN) version of a Brassica napus MPK4 (BnMPK4) in Nicotiana benthamiana leaves. Proteomics analysis revealed that BnMPK4 activation affects multiple pathways (e.g., metabolism, redox regulation, jasmonic acid biosynthesis and stress responses). Furthermore, BnMPK4 activation also increased protein phosphorylation in the phosphoproteome, from which putative MPK4 substrates were identified. Using protein kinase assay, we validated that a transcription factor TCP8-like (TCP8) and a PP2A regulatory subunit TAP46-like (TAP46) were indeed phosphorylated by BnMPK4. Taken together, we demonstrated the utility of proteomics and phosphoproteomics in elucidating kinase signaling networks and inidentification of downstream substrates.

Spermine Confers Stress Resilience by Modulating Abscisic Acid Biosynthesis and Stress Responses in Arabidopsis Plants.

Polyamines (PAs) constitute a group of low molecular weight aliphatic amines that have been implicated as key players in growth and development processes, as well as in the response to biotic and abiotic stresses. Transgenic plants overexpressing PA-biosynthetic genes show increased tolerance to abiotic stress. Therein, abscisic acid (ABA) is the hormone involved in plant responses to environmental stresses such as drought or high salinity. An increase in the level of free spermine (Spm) in transgenic Arabidopsis plants resulted in increased levels of endogenous ABA and promoted, in a Spm-dependent way, transcription of different ABA inducible genes. This phenotype was only partially reversed by blocking ABA biosynthesis, indicating an ABA independent response mediated by Spm. Moreover, the phenotype was reproduced by adding Spm to Col0 wild-type Arabidopsis plants. In contrast, Spm-deficient mutants showed a lower tolerance to salt stress. These results indicate that Spm plays a key role in modulating plant stress responses.

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.

MgrB affects the acid stress response of Escherichia coli by modulating the expression of iraM.

Although MgrB is established to be a feedback inhibitor of the PhoP/Q system in Escherichia coli, the biological functions of MgrB remain largely unknown. To explore new functions of MgrB, a comparative transcriptome analysis was performed (E. coli K-12 W3110 ΔmgrB vs E. coli K-12 W3110). The results showed that many genes involved in acid stress are upregulated, suggesting that MgrB is related to acid sensitivity in E. coli. The survival rates under acid stress of the ΔmgrB mutant and wild-type showed that deletion of mgrB resulted in acid resistance. According to previous research, we deleted phoP, phoQ and iraM in the ΔmgrB mutant, and found that further deletion of phoP/phoQ only partially restored acid sensitivity. Additionally, we found that deletion of mgrB resulted in increased accumulation of RpoS during the exponential growth phase, which could be blocked by further deletion of iraM. Mutation of iraM or rpoS completely suppressed the effect of mgrB mutation on acid resistance. Taken together, the data suggest that MgrB affects the acid resistance of E. coli by modulating the expression of iraM, but not completely through PhoP/Q. This indicates that MgrB may have other protein interactors aside from PhoQ, which merits further investigation.

Unveiling the acid stress response of clinical genotype Vibrio vulnificus isolated from the marine environments of Mangaluru coast, India.

Gastric acidity is one of the earliest host defences faced by ingested organisms, and successful pathogens need to overcome this hurdle. The objective of this study was the systematic assessment of acid-stress response of Vibrio vulnificus isolated from coastal regions of Mangaluru. Acid-shock experiments were carried out at pH 4.0 and pH 4.5, with different experimental conditions expected to produce a varied acid response. Exposure to mild acid before the acid shock was favourable to the bacteria but was dependent on cell population and pH of the media and was independent of the strains tested. Lysine-dependent acid response was demonstrated with reference to the previously identified lysine decarboxylase system. Additionally, the results showed that inoculation into oysters provided some level of protection against acid stress. Increased expression of lysine/cadaverine genes was observed upon the addition of ground oyster and was confirmed by quantitative real-time PCR. The potential role of ornithine was analyzed with regard to acid stress, but no change in the survival pattern was observed. These findings highlight the physiology of bacteria in acid stress.

Regulation and role of the ER stress transcription factor CHOP in alveolar epithelial type-II cells

Idiopathic pulmonary fibrosis (IPF) is a fatal disease characterized by type-II alveolar epithelial cell (AECII) injury and fibroblast hyperproliferation. Severe AECII endoplasmic reticulum (ER) stress is thought to underlie IPF, but is yet incompletely understood. We studied the regulation of C/EBP homologous protein (CHOP), a proapoptotic ER-stress-related transcription factor (TF) in AECII-like cells. Interestingly, single or combined overexpression of the active ER stress transducers activating transcription factor-4 (Atf4) and activating transcription factor-6 (p50Atf6) or spliced x-box-binding protein-1 (sXbp1) in MLE12 cells did not result in a substantial Chop induction, as compared to the ER stress inducer thapsigargin. Employing reporter gene assays of distinct CHOP promoter fragments, we could identify that, next to the conventional amino acid (AARE) and ER stress response elements (ERSE) within the CHOP promoter, activator protein-1 (AP-1) and c-Ets-1 TF binding sites are necessary for CHOP induction. Serial deletion and mutation analyses revealed that both AP-1 and c-Ets-1 motifs act in concert to induce CHOP expression. In agreement, CHOP promoter activity was greatly enhanced upon combined versus single overexpression of AP-1 and c-Ets-1. Moreover, combined overexpression of AP-1 and c-Ets-1 in MLE12 cells alone in the absence of any other ER stress inducer was sufficient to induce Chop protein expression. Further, AP-1 and c-Ets-1 were upregulated in AECII under ER stress conditions and in human IPF. Finally, Chop overexpression in vitro resulted in AECII apoptosis, lung fibroblast proliferation, and collagen-I production. We propose that CHOP activation by AP-1 and c-Ets-1 plays a key role in AECII maladaptive ER stress responses and consecutive fibrosis, offering new therapeutic prospects in IPF.Key messagesOverexpression of active ER stress sensors Atf4, Atf6, and Xbp1 does not induce Chop.AP-1 and c-Ets-1 TFs are necessary for induction of the ER stress factor Chop.AP-1 and c-Ets-1 alone induce Chop expression in the absence of any ER stress inducers.AP-1 and c-Ets-1 are induced in AECII under ER stress conditions and in human IPF.Chop expression alone triggers AECII apoptosis and consecutive profibrotic responses.

Transcriptomic response of Escherichia coli O157 isolates on meat: Comparison between a typical Australian isolate from cattle and a pathogenic clinical isolate

The majority of foodborne illnesses associated with E. coli O157 are attributed to the consumption of foods of bovine origin. In this study, RNA-Seq experiments were undertaken with E. coli O157 to identify genes that may be associated with growth and survival on meat and the beef carcass at low temperature. In addition, the response of an E. coli O157 isolate representative of the general genetic ‘type’ found in Australia (E. coli O157:H− strain EC2422) was compared to that of a pathogenic clinical isolate (E. coli O157:H7 strain Sakai) not typically found in Australia. Both strains up-regulated genes involved in the acid stress response, cold shock response, quorum sensing, biofilm formation and Shiga toxin production. Differences were also observed, with E. coli O157:H7 Sakai up-regulating genes playing a critical role in the barrier function of the outer membrane, lipopolysaccharide biosynthesis, extracellular polysaccharide synthesis and curli production. In contrast, E. coli O157:H− EC2422 down-regulated genes involved in peptidoglycan biosynthesis and of the primary envelope stress response Cpx system. The unique gene expression profiles of the strains, indicate that these genotypes may differ in their ability to persist in the meat production environment and therefore also in their ability to cause disease.

RcsB regulation of the YfdX-mediated acid stress response in Klebsiella pneumoniae CG43S3.

In Klebsiella pneumoniae CG43S3, deletion of the response regulator gene rcsB reduced the capsular polysaccharide amount and survival on exposure to acid stress. A comparison of the pH 4.4-induced proteomes between CG43S3 and CG43S3ΔrcsB revealed numerous differentially expressed proteins and one of them, YfdX, which has recently been reported as a periplasmic protein, was absent in CG43S3ΔrcsB. Acid survival analysis was then conducted to determine its role in the acid stress response. Deletion of yfdX increased the sensitivity of K. pneumoniae CG43S3 to a pH of 2.5, and transforming the mutant with a plasmid carrying yfdX restored the acid resistance (AR) levels. In addition, the effect of yfdX deletion was cross-complemented by the expression of the periplasmic chaperone HdeA. Furthermore, the purified recombinant protein YfdX reduced the acid-induced protein aggregation, suggesting that YfdX as well as HdeA functions as a chaperone. The following promoter activity measurement revealed that rcsB deletion reduced the expression of yfdX after the bacteria were subjected to pH 4.4 adaptation. Western blot analysis also revealed that YfdX production was inhibited by rcsB deletion and only the plasmid expressing RcsB or the nonphosphorylated form of RcsB, RcsBD56A, could restore the YfdX production, and the RcsB-mediated complementation was no longer observed when the sensor kinase RcsD gene was deleted. In conclusion, this is the first study demonstrating that YfdX may be involved in the acid stress response as a periplasmic chaperone and that RcsB positively regulates the acid stress response partly through activation of yfdX expression. Moreover, the phosphorylation status of RcsB may affect the YfdX expression under acidic conditions.

Differential View on the Bile Acid Stress Response of Clostridioides difficile.

Clostridioides difficile is an intestinal human pathogen that uses the opportunity of a depleted microbiota to cause an infection. It is known, that the composition of the intestinal bile acid cocktail has a great impact on the susceptibility toward a C. difficile infection. However, the specific response of growing C. difficile cells to diverse bile acids on the molecular level has not been described yet. In this study, we recorded proteome signatures of shock and long-term (LT) stress with the four main bile acids cholic acid (CA), chenodeoxycholic acid (CDCA), deoxycholic acid (DCA), and lithocholic acid (LCA). A general overlapping response to all tested bile acids could be determined particularly in shock experiments which appears plausible in the light of their common steroid structure. However, during LT stress several proteins showed an altered abundance in the presence of only a single or a few of the bile acids indicating the existence of specific adaptation mechanisms. Our results point at a differential induction of the groEL and dnaKJgrpE chaperone systems, both belonging to the class I heat shock genes. Additionally, central metabolic pathways involving butyrate fermentation and the reductive Stickland fermentation of leucine were effected, although CA caused a proteome signature different from the other three bile acids. Furthermore, quantitative proteomics revealed a loss of flagellar proteins in LT stress with LCA. The absence of flagella could be substantiated by electron microscopy which also indicated less flagellated cells in the presence of DCA and CDCA and no influence on flagella formation by CA. Our data break down the bile acid stress response of C. difficile into a general and a specific adaptation. The latter cannot simply be divided into a response to primary and secondary bile acids, but rather reflects a complex and variable adaptation process enabling C. difficile to survive and to cause an infection in the intestinal tract.

Suberin and hemicellulose in sugarcane cell wall architecture and crop digestibility: A biotechnological perspective

AbstractSugarcane is a highly efficient biomass producer used in the last decades for bioethanol and bioelectricity production, as well as for animal feeding. Together with lignin, suberin is a major factor for the low sugarcane biomass digestibility by ruminants. The lipid–phenolic biomolecular composition and the ultrastructure of suberin and associated waxes confer them extraordinary properties of hydrophobicity, flexibility, and anti‐microbial resistance, responsible for the low digestibility of suberized tissues. Additionally, hemicelluloses cross‐linked with suberin and lignin also contribute appreciably to cell wall recalcitrance. In this review, a main focus was given to suberin and secondly to hemicellulose and how they may interfere with ruminant digestibility. Suberin and hemicellulose deposition and biomolecular composition are genetically regulated, showing a close regulatory interplay with phenylpropanoid and fatty acid biosynthesis pathways, cutin disruption, and stress and defense responses. Understanding the bulk of transcription factors network and hormonal regulatory mechanisms will allow accurate biotechnological approaches to the production of more feasible forage sugarcane.