Transcriptome analysis of adaptive heat shock response of Streptococcus thermophilus

When the going gets tough, the tough get going-Novel bacterial AAA+ disaggregases provide extreme heat resistance

Heat stress can lead to protein misfolding and aggregation, potentially causing cell death due to the loss of essential proteins. Bacteria, being particularly exposed to environmental stress, are equipped with disaggregases that rescue these aggregated proteins. The bacterial Hsp70 chaperone DnaK and the ATPase associated with diverse cellular activities protein ClpB form the canonical disaggregase in bacteria. While this combination operates effectively during physiological heat stress, it is ineffective against massive aggregation caused by temperature-based sterilization protocols used in the food industry and clinics. This leaves bacteria unprotected against these thermal processes. However, bacteria that can withstand extreme, man-made stress conditions have emerged. These bacteria possess novel ATPase associated with diverse cellular activities disaggregases, ClpG and ClpL, which are key players in extreme heat resistance. These disaggregases, present in selected Gram-negative or Gram-positive bacteria, respectively, function superiorly by exhibiting increased thermal stability and enhanced threading power compared to DnaK/ClpB. This enables ClpG and ClpL to operate at extreme temperatures and process large and tight protein aggregates, thereby contributing to heat resistance. The genes for ClpG and ClpL are often encoded on mobile genomic islands or conjugative plasmids, allowing for their rapid spread among bacteria via horizontal gene transfer. This threatens the efficiency of sterilization protocols. In this review, we describe the various bacterial disaggregases identified to date, characterizing their commonalities and the specific features that enable these novel disaggregases to provide stress protection against extreme stress conditions.

The Listeria monocytogenes persistence factor ClpL is a potent stand-alone disaggregase

Heat stress can cause cell death by triggering the aggregation of essential proteins. In bacteria, aggregated proteins are rescued by the canonical Hsp70/AAA+ (ClpB) bi-chaperone disaggregase. Man-made, severe stress conditions applied during, e.g., food processing represent a novel threat for bacteria by exceeding the capacity of the Hsp70/ClpB system. Here, we report on the potent autonomous AAA+ disaggregase ClpL from Listeria monocytogenes that provides enhanced heat resistance to the food-borne pathogen enabling persistence in adverse environments. ClpL shows increased thermal stability and enhanced disaggregation power compared to Hsp70/ClpB, enabling it to withstand severe heat stress and to solubilize tight aggregates. ClpL binds to protein aggregates via aromatic residues present in its N-terminal domain (NTD) that adopts a partially folded and dynamic conformation. Target specificity is achieved by simultaneous interactions of multiple NTDs with the aggregate surface. ClpL shows remarkable structural plasticity by forming diverse higher assembly states through interacting ClpL rings. NTDs become largely sequestered upon ClpL ring interactions. Stabilizing ring assemblies by engineered disulfide bonds strongly reduces disaggregation activity, suggesting that they represent storage states.

Unravelling the transcriptome response of Enterobacter sp. S-33 under varying temperature

Enterobacter genus includes the bacteria occupying every aspect of environment, however, their adaptability at varying temperature is not clear. In the present study, we analyzed the transcriptome response of Enterobacter sp. S-33 and their functional genes under various temperatures (30-45 ℃) that were expressed and accumulated in cells under temperature-stress. During a temperature shift from 37 to 45 ℃, 165 genes showed differential expression including 112 up-regulated and 53 down-regulated. In particular, heat-shock genes such as CspA, 16 kDa heat shock protein A/B and transcriptional regulators such as LysR, TetR, and LuxR were differentially expressed, indicating the role of complex molecular mechanism of Enterobacter adapting to temperature stress. Similarly, genes associated to signal transduction, ABC transporters, iron homeostasis, and quorum sensing were also induced. The Gene ontology enrichment analysis of differentially expressed genes (DEGs) were categorized into "transmembrane transport", "tRNA binding", "hydrogen sulfide biosynthetic process" and "sulfate assimilation" terms. In addition, Kyoto Encyclopedia of Genes and Genomes pathways showed that ABC transporter as well as quorum sensing pathways were significantly enriched. Overall, current study has contributed to explore the adaptive molecular mechanisms of Enterobacter spp. upon temperature change, which further opens new avenues for future in-depth functional studies.

Effects of different carbon sources on metabolic profiles of carbohydrates in Streptococcus thermophilus during fermentation

BACKGROUND

Streptococcus thermophilus is a major starter used in the dairy industry and it could improve the flavor of fermented products. It is necessary to improve biomass of S. thermophilus for its application and industrialization. The utilization of carbon sources directly affects the biomass of S. thermophilus. Therefore, the carbohydrate metabolism of S. thermophilus should be investigated.

RESULTS

In the present study, metabolic parameters and gene expression of S. thermophilus S-3 with different carbon sources were investigated. The physicochemical results showed that S. thermophilus S-3 had high lactose utilization. Transcriptome analysis found that approximately 104 genes were annotated onto 15 carbohydrate metabolic pathways, of which 15 unigenes were involved in the phosphotransferase system and 75 were involved in the ATP-binding cassette transporter system. In addition, 171 differentially expressed genes related to carbohydrate metabolism were identified. Expression of the galactose metabolism genes lacSZ and galKTEM increased significantly from the lag phase to the mid-exponential growth phase as a result of the global regulator protein, catabolite control protein A (CcpA). The high expression of galK in the mid- to late- phases indicated that the metabolite galactose is re-transported for intracellular utilization. CcpA regulation may also induce high expressions of glycolytic pathway regulated-genes related to lactose utilization, including ldh, fba, eno, pfkA, bglA, pgi, pgm and pyk, producing optimal glycolytic flux and S. thermophilus S-3 growth.

CONCLUSION

The present study provides new insights into the carbon metabolism regulation and provide theoretical support for high-density fermentation of S. thermophilus S-3. © 2022 Society of Chemical Industry.

Genome-Scale Metabolic Modeling Combined with Transcriptome Profiling Provides Mechanistic Understanding of Streptococcus thermophilus CH8 Metabolism

Streptococcus thermophilus is a lactic acid bacterium adapted toward growth in milk and is a vital component of starter cultures for milk fermentation. Here, we combine genome-scale metabolic modeling and transcriptome profiling to obtain novel metabolic insights into this bacterium. Notably, a refined genome-scale metabolic model (GEM) accurately representing S. thermophilus CH8 metabolism was developed. Modeling the utilization of casein as a nitrogen source revealed an imbalance in amino acid supply and demand, resulting in growth limitation due to the scarcity of specific amino acids, in particular sulfur amino acids. Growth experiments in milk corroborated this finding. A subtle interdependency of the redox balance and the secretion levels of the key metabolites lactate, formate, acetoin, and acetaldehyde was furthermore identified with the modeling approach, providing a mechanistic understanding of the factors governing the secretion product profile. As a potential effect of high expression of arginine biosynthesis genes, a moderate secretion of ornithine was observed experimentally, augmenting the proposed hypothesis of ornithine/putrescine exchange as part of the protocooperative interaction between S. thermophilus and Lactobacillus delbrueckii subsp. bulgaricus in yogurt. This study provides a foundation for future community modeling of food fermentations and rational development of starter strains with improved functionality.

IMPORTANCEStreptococcus thermophilus is one the main organisms involved in the fermentation of milk and, increasingly, also in the fermentation of plant-based foods. The construction of a functional high-quality genome-scale metabolic model, in conjunction with in-depth transcriptome profiling with a focus on metabolism, provides a valuable resource for the improved understanding of S. thermophilus physiology. An example is the model-based prediction of the most significant route of synthesis for the characteristic yogurt flavor compound acetaldehyde and identification of metabolic principles governing the synthesis of other flavor compounds. Moreover, the systematic assessment of amino acid supply and demand during growth in milk provides insights into the key challenges related to nitrogen metabolism that is imposed on S. thermophilus and any other organism associated with the milk niche.

Omics Approaches to Assess Flavor Development in Cheese

Cheese is characterized by a rich and complex microbiota that plays a vital role during both production and ripening, contributing significantly to the safety, quality, and sensory characteristics of the final product. In this context, it is vital to explore the microbiota composition and understand its dynamics and evolution during cheese manufacturing and ripening. Application of high-throughput DNA sequencing technologies have facilitated the more accurate identification of the cheese microbiome, detailed study of its potential functionality, and its contribution to the development of specific organoleptic properties. These technologies include amplicon sequencing, whole-metagenome shotgun sequencing, metatranscriptomics, and, most recently, metabolomics. In recent years, however, the application of multiple meta-omics approaches along with data integration analysis, which was enabled by advanced computational and bioinformatics tools, paved the way to better comprehension of the cheese ripening process, revealing significant associations between the cheese microbiota and metabolites, as well as their impact on cheese flavor and quality.

Properties of Modestobacter deserti sp. nov., a Kind of Novel Phosphate-Solubilizing Actinobacteria Inhabited in the Desert Biological Soil Crusts

Three Gram-stain-positive, aerobic, motile actinobacterial strains designated as CPCC 205119^T, CPCC 205215, and CPCC 205251 were isolated from different biological soil crust samples collected from Tengger Desert, China. The 16S rRNA gene sequence comparison of these three strains showed they had almost identical 16S rRNA genes, which were closely related to members of the family Geodermatophilaceae, with the highest similarities of 96.3–97.3% to the species of Modestobacter. In the phylogenetic tree based on 16S rRNA gene sequences, these isolates clustered into a subclade next to the branch containing the species of Modestobacter lapidis and Modestobacter multiseptatus, within the lineage of the genus Modestobacter. The comparative genomic characteristics (values of ANI, dDDH, AAI, and POCP) and the phenotypic properties (morphological, physiological, and chemotaxonomic characteristics) of these isolates readily supported to affiliate them to the genus Modestobacter as a single separate species. For which, we proposed that the isolates CPCC 205119^T, CPCC 205215, and CPCC 205251 represent a novel species of the genus Modestobacter as Modestobacter deserti sp. nov. CPCC 205119^T (=I12A-02624=NBRC 113528^T=KCTC 49201^T) is the type strain. The genome of strain CPCC 205119^T consisted of one chromosome (4,843,235bp) containing 4,424 coding genes, 48 tRNA genes, five rRNA genes, three other ncRNA genes, and 101 pseudogenes, with G+C content of 74.7%. The whole-genome sequences analysis indicated that this species contained alkaline phosphatase genes (phoA/phoD), phosphate transport-related genes (phoU, phnC, phnD, phnE, phoB, phoH, phoP, phoR, pitH, ppk, pstA, pstB, pstC, and pstS), trehalose-phosphate synthase gene (otsA), trehalose 6-phosphate phosphatase gene (otsB) and other encoding genes for the properties that help the microorganisms to adapt to harsh environmental conditions prevalent in deserts. Strains of this species could solubilize tricalcium phosphate [Ca₃(PO₄)₂] and phytin, assimilate pyrophosphate, thiophosphate, dithiophosphate, phosphoenol pyruvate, 2-deoxy-d-glucose-6-phosphate, and cysteamine-S-phosphate.

Effect of High Hydrostatic Pressure on Stress-Related dnaK, hrcA, and ctsR Expression Patterns in Selected Lactobacilli Strains

Lactic acid bacteria (LAB) in the natural environment meet multiple stressors such as pH and temperature variations, increased nutrition and metabolite concentrations, harmful chemicals, acidic/oxidative conditions, osmotic pressure, and starvation. However, LAB strains are not subjected to high hydrostatic pressure (HHP) which currently is the most common non-thermal decontamination technology in the food industry. In this context, the LAB response to HHP is more difficult to identify compared to other stress-induced responses, and dnaK, ctsR, and hrcA can serve as essential regulators in this reaction. In the present study, the expression level of dnaK, ctsR, and hrcA mRNAs in 15 LAB strains after the HHP (300 MPa/5′) exposure was evaluated. As a result, the HHP-treatment affected the up-regulation of dnaK, ctsR, and hrcA in L. backii KKP 3565, L. backii KKP 3566, L. rhamnosus KKP 3570, L. brevis KKP 3575 strains, whereas, in L. plantarum KKP 3569, L. rhamnosus KKP 3571, L. brevis KKP 3573 all genes were lower expressed. The relative expression level of the dnaK, ctsR, and hrcA either before or after the pressure treatment for L. brevis DSM 6235, L. rhamnosus KKP 3572, L. brevis KKP 3574, L. brevis KKP 3576, L. rossiae KKP 3577, L. curvatus KKP 3578 strains were undetectable. Significant differences in the expression levels were observed, between the control and the HHP treatment strains for dnaK in L. backii KKP 3565, L. backii KKP 3566, L. plantarum KKP 3569, L. rhamnosus KKP 3570, L. rhamnosus KKP 3571, ctsR in, L. backii KKP 3565, L. rhamnosus KKP 3570, L. rhamnosus KKP 3571, and hrcA in L. plantarum KKP 3569, L. rhamnosus KKP 3571. Overall, the studied genes, dnaK, ctsR, and hrcA can be useful markers to indicate the LAB cellular response to HHP. These molecular parameters can help to optimize the desirable LAB growing conditions in industrial processes and to understand the complexity of the stress-related mechanism.

Complete Genome Sequence of the Newly Developed Lactobacillus acidophilus Strain With Improved Thermal Adaptability

Lactobacillus acidophilus (L. acidophilus) is a representative probiotic and is widely used in many industrial products for its beneficial effects on human and animal health. This bacterium is exposed to harsh environments such as high temperatures for manufacturing industrial products, but cell yield under high temperatures is relatively low. To resolve this issue, we developed a new L. acidophilus strain with improved heat resistance while retaining the existing beneficial properties through the adaptive laboratory evolution (ALE) method. The newly developed strain, L. acidophilus EG008, has improved the existing limit of thermal resistance from 65°C to 75°C. Furthermore, we performed whole-genome sequencing and comparative genome analysis of wild-type and EG008 strains to unravel the molecular mechanism of improved heat resistance. Interestingly, only two single-nucleotide polymorphisms (SNPs) were different compared to the L. acidophilus wild-type. We identified that one of these SNPs is a non-synonymous SNP capable of altering the structure of MurD protein through the 435th amino acid change from serine to threonine. We believe that these results will directly contribute to any industrial field where L. acidophilus is applied. In addition, these results make a step forward in understanding the molecular mechanisms of lactic acid bacteria evolution under extreme conditions.

Resisting the Heat: Bacterial Disaggregases Rescue Cells From Devastating Protein Aggregation

Bacteria as unicellular organisms are most directly exposed to changes in environmental growth conditions like temperature increase. Severe heat stress causes massive protein misfolding and aggregation resulting in loss of essential proteins. To ensure survival and rapid growth resume during recovery periods bacteria are equipped with cellular disaggregases, which solubilize and reactivate aggregated proteins. These disaggregases are members of the Hsp100/AAA+ protein family, utilizing the energy derived from ATP hydrolysis to extract misfolded proteins from aggregates via a threading activity. Here, we describe the two best characterized bacterial Hsp100/AAA+ disaggregases, ClpB and ClpG, and compare their mechanisms and regulatory modes. The widespread ClpB disaggregase requires cooperation with an Hsp70 partner chaperone, which targets ClpB to protein aggregates. Furthermore, Hsp70 activates ClpB by shifting positions of regulatory ClpB M-domains from a repressed to a derepressed state. ClpB activity remains tightly controlled during the disaggregation process and high ClpB activity states are likely restricted to initial substrate engagement. The recently identified ClpG (ClpK) disaggregase functions autonomously and its activity is primarily controlled by substrate interaction. ClpG provides enhanced heat resistance to selected bacteria including pathogens by acting as a more powerful disaggregase. This disaggregase expansion reflects an adaption of bacteria to extreme temperatures experienced during thermal based sterilization procedures applied in food industry and medicine. Genes encoding for ClpG are transmissible by horizontal transfer, allowing for rapid spreading of extreme bacterial heat resistance and posing a threat to modern food production.

Heat-responsive and time-resolved transcriptome and metabolome analyses of Escherichia coli uncover thermo-tolerant mechanisms

Current understanding of heat shock response has been complicated by the fact that heat stress is inevitably accompanied by changes in specific growth rates and growth stages. In this study, a chemostat culture was successfully performed to avoid the physico-chemical and biological changes that accompany heatshock, which provided a unique opportunity to investigate the full range of cellular responses to thermal stress, ranging from temporary adjustment to phenotypic adaptation at multi-omics levels. Heat-responsive and time-resolved changes in the transcriptome and metabolome of a widely used E. coli strain BL21(DE3) were explored in which the temperature was upshifted from 37 to 42 °C. Omics profiles were categorized into early (2 and 10 min), middle (0.5, 1, and 2 h), and late (4, 8, and 40 h) stages of heat stress, each of which reflected the initiation, adaptation, and phenotypic plasticity steps of the stress response. The continued heat stress modulated global gene expression by controlling the expression levels of sigma factors in different time frames, including unexpected downregulation of the second heatshock sigma factor gene (rpoE) upon the heat stress. Trehalose, cadaverine, and enterobactin showed increased production to deal with the heat-induced oxidative stress. Genes highly expressed at the late stage were experimentally validated to provide thermotolerance. Intriguingly, a cryptic capsular gene cluster showed considerably high expression level only at the late stage, and its expression was essential for cell growth at high temperature. Granule-forming and elongated cells were observed at the late stage, which was morphological plasticity occurred as a result of acclimation to the continued heat stress. Whole process of thermal adaptation along with the genetic and metabolic changes at fine temporal resolution will contribute to far-reaching comprehension of the heat shock response. Further, the identified thermotolerant genes will be useful to rationally engineer thermotolerant microorganisms.

Modestobacter altitudinis sp. nov., a novel actinobacterium isolated from Atacama Desert soil

Three presumptive Modestobacter strains isolated from a high altitude Atacama Desert soil were the subject of a polyphasic study. The isolates, strains 1G4^T, 1G51 and 1G52, were found to have chemotaxonomic and morphological properties that were consistent with their assignment to the genus Modestobacter. They formed a well supported clade in Modestobacter 16S rRNA gene trees and were most closely related to the type strain of 'Modestobacter excelsi' (99.8-99.9% similarity). They were also closely related to the type strains of Modestobacter caceresii (99.6 % similarity), Modestobacter italicus (99.7-99.9% similarity), Modestobacter lacusdianchii (98.4-99.2% similarity), Modestobacter marinus (99.4-99.5% similarity) and Modestobacter roseus (99.3-99.5% similarity), but were distinguished from their closest relatives by a combination of phenotypic features. Average nucleotide identity and digital DNA:DNA hybridization similarities drawn from comparisons of draft genome sequences of isolate 1G4^T and its closest phylogenetic neighbours mentioned above, were well below the threshold used to assign closely related strains to the same species. The close relationship between isolate 1G4^T and the type strain of M. excelsi was showed in a phylogenomic tree containing representative strains of family Geodermatophilaceae. The draft genome sequence of isolate 1G4^T (size 5.18 Kb) was shown to be rich in stress related genes providing further evidence that the abundance of Modestobacter propagules in Atacama Desert habitats reflects their adaptation to the harsh environmental conditions prevalent in this biome. In light of all of these data it is proposed that the isolates be assigned to a novel species in the genus Modestobacter. The name proposed for this taxon is Modestobacter altitudinis sp. nov., with isolate 1G4^T (=DSM 107534^T=PCM 3003^T) as the type strain.

Transcriptome Analysis of Gene Expression in Dermacoccus abyssi HZAU 226 under Lysozyme Stress

Lysozyme acts as a kind of cationic antimicrobial protein and effectively hydrolyzes bacterial peptidoglycan to have a bactericidal effect, which also plays an important role in protecting eggs from microbial contamination. Dermacoccus abyssi HZAU 226, a Gram-positive bacterium isolated from spoiled eggs, has egg white and lysozyme tolerance, but its survival mechanism is unknown, especially from a transcriptomics point of view. In this study, the high lysozyme tolerance of D. abyssi HZAU 226 was characterized by three independent experiments, and then the Illumina RNA-seq was used to compare the transcriptional profiles of this strain in Luria–Bertani (LB) medium with and without 5 mg/mL lysozyme to identify differentially expressed genes (DEGs); 1024 DEGs were identified by expression analysis, including 544 up-regulated genes and 480 down-regulated genes in response to lysozyme treatment. The functional annotation analysis results of DEGs showed that these genes were mainly involved in glutathione biosynthesis and metabolism, ion transport, energy metabolism pathways, and peptidoglycan biosynthesis. This study is the first report of bacterial-related lysozyme RNA-seq, and our results help in understanding the lysozyme-tolerance mechanism of bacteria from a new perspective and provide transcriptome resources for subsequent research in related fields.

Adaptation of Lactobacillus plantarum to Ampicillin Involves Mechanisms That Maintain Protein Homeostasis

The widespread use of antibiotics has caused great concern in the biosafety of probiotics. In this study, we conducted a 12-month adaptive laboratory evolution (ALE) experiment to select for antibiotics-adapted Lactobacillus plantarum P-8, a dairy-originated probiotic bacterium. During the ALE process, the ampicillin MIC for the parental L. plantarum P-8 strain increased gradually and reached the maximum level of bacterial fitness. To elucidate the molecular mechanisms underlying the ampicillin-resistant phenotype, we comparatively analyzed the genomes and proteomes of the parental strain (L. plantarum P-8) and two adapted lines (L. plantarum 400g and L. plantarum 1600g). The adapted lines showed alterations in their carbon, amino acid, and cell surface-associated metabolic pathways. Then, gene disruption mutants were created to determine the role of six highly expressed genes in contributing to the enhanced ampicillin resistance. Inactivation of an ATP-dependent Clp protease/the ATP-binding subunit ClpL, a small heat shock protein, or a hypothetical protein resulted in partial but significant phenotypic reversion, confirming their necessary roles in the bacterial adaptation to ampicillin. Genomic analysis confirmed that none of the ampicillin-specific differential expressed genes were flanked by any mobile genetic elements; thus, even though long-term exposure to ampicillin upregulated their expression, there is low risk of spread of these genes and adapted drug resistance to other bacteria via horizontal gene transfer. Our study has provided evidence of the biosafety of probiotics even when used in the presence of antibiotics.IMPORTANCE Antibiotic resistance acquired by adaptation to certain antibiotics has led to growing public concerns. Here, a long-term evolution experiment was used together with proteomic analysis to identify genes/proteins responsible for the adaptive phenotype. This work has provided novel insights into the biosafety of new probiotics with high tolerance to antibiotics.

Blastococcus atacamensis sp. nov., a novel strain adapted to life in the Yungay core region of the Atacama Desert

A polyphasic study was undertaken to establish the taxonomic status of a Blastococcus strain isolated from an extreme hyper-arid Atacama Desert soil. The isolate, strain P6^T, was found to have chemotaxonomic and morphological properties consistent with its classification in the genus Blastococcus. It was shown to form a well-supported branch in the Blastococcus 16S rRNA gene tree together with the type strains of Blastococcus capsensis and Blastococcus saxobsidens and was distinguished from the latter, its close phylogenetic neighbour, by a broad range of phenotypic properties. The draft genome sequence of isolate P6^T showed 84.6 % average nucleotide identity, 83.0 % average amino acid identity and a digital DNA-DNA hybridisation value of 27.8 % in comparison with the genome sequence of B. saxobsidens DSM 44509^T, values consistent with its assignment to a separate species. Based on these data it is proposed that isolate P6^T (NCIMB 15090^T=NRRL B-65468^T) be assigned to the genus Blastococcus as Blastococcus atacamensis sp. nov. Analysis of the whole genome sequence of B. atacamensis P6^T, with 3778 open reading frames and a genome size of 3.9 Mb showed the presence of genes and gene clusters that encode for properties that reflect its adaptation to the extreme environmental conditions that prevail in Atacama Desert soils.

A Capsular Polysaccharide-Specific Antibody Alters Streptococcus pneumoniae Gene Expression during Nasopharyngeal Colonization of Mice

Pneumococcal conjugate vaccines (PCV) elicit opsonophagocytic (opsonic) antibodies to pneumococcal capsular polysaccharides (PPS) and reduce nasopharyngeal (NP) colonization by vaccine-included Streptococcus pneumoniae serotypes. However, nonopsonic antibodies may also be important for protection against pneumococcal disease. For example, 1E2, a mouse IgG1 monoclonal antibody (MAb) to the serotype 3 (ST3) PPS (PPS3), reduced ST3 NP colonization in mice and altered ST3 gene expression in vitro Here, we determined whether 1E2 affects ST3 gene expression in vivo during colonization of mice by performing RNA sequencing on NP lavage fluid from ST3-infected mice treated with 1E2, a control MAb, or phosphate-buffered saline. Compared to the results for the controls, 1E2 significantly altered the expression of over 50 genes. It increased the expression of the piuBCDA operon, which encodes an iron uptake system, and decreased the expression of dpr, which encodes a protein critical for resistance to oxidative stress. 1E2-mediated effects on ST3 in vivo required divalent binding, as Fab fragments did not reduce NP colonization or alter ST3 gene expression. In vitro, 1E2 induced dose-dependent ST3 growth arrest and altered piuB and dpr expression, whereas an opsonic PPS3 MAb, 5F6, did not. 1E2-treated bacteria were more sensitive to hydrogen peroxide and the iron-requiring antibiotic streptonigrin, suggesting that 1E2 may increase iron import and enhance sensitivity to oxidative stress. Finally, 1E2 also induced rapid capsule shedding in vitro, suggesting that this may initiate 1E2-induced changes in sensitivity to oxidative stress and gene expression. Our data reveal a novel mechanism of direct, antibody-mediated antibacterial activity that could inform new directions in antipneumococcal therapy and vaccine development.

Comparative mRNA-Seq Analysis Reveals the Improved EPS Production Machinery in Streptococcus thermophilus ASCC 1275 During Optimized Milk Fermentation

Exo-polysaccharide (EPS) produced by dairy starters plays critical roles in improving texture and functionalities of fermented dairy products. One of such high EPS producers, Streptococcus thermophilus ASCC 1275 (ST1275) was used as a model dairy strain to understand the stimulation of its EPS production under optimal milk fermentation conditions. The mRNA-seq analysis and targeted pathway analysis indicate that genes associated with lactose (milk sugar) catabolism, EPS assembly, proteolytic activity, and arginine/methionine/cysteine synthesis and transport in ST1275 were significantly up-regulated under the optimized conditions of pH 5.5, 40°C, or WPI supplementation compared to that of pH 6.5 and 37°C, respectively. This indicates that genes involved in above metabolisms cooperate together for improving EPS yield from ST1275. This study provides a global view map on potential targeted pathways and specific genes accounted for enhanced EPS production in Str. thermophilus and that could be modulated by fermentation conditions.

Biofilm formation and transcriptome analysis of Streptococcus gallolyticus subsp. gallolyticus in response to lysozyme

Streptococcus gallolyticus subsp. gallolyticus is a commensal bacterium of the human gastrointestinal tract, and a pathogen causing infective endocarditis and other biofilm-associated infections via exposed collagen. This study focuses on the characterization of the biofilm formation and collagen adhesion of S. gallolyticus subsp. gallolyticus under different conditions. In this study, it has been observed that the isolate UCN 34 is resistant to 20 mg/ml lysozyme in BHI medium, whereas the strain BAA-2069 builds more biofilm in the presence of lysozyme compared to in a control of BHI without lysozyme. A transcriptome analysis with whole genome microarrays of these two isolates in BHI medium with lysozyme compared to control without lysozyme revealed changes in gene expression levels. In the isolate BAA-2069, 67 genes showed increased expression in the presence of lysozyme, while in the isolate UCN 34, 165 genes showed increased expression and 30 genes showed decreased expression through lysozyme treatment. Products of genes which were higher expressed are in involved in transcription and translation, in cell-wall modification, in hydrogen peroxide resistance and in bacterial immunity. Furthermore, the adhesion ability of different strains of S. gallolyticus subsp. gallolyticus to collagen type I and IV was analyzed. Thereby, we compared the adhesion of 46 human isolates with 23 isolates from animals. It was shown that the adhesion ability depends significantly on whether the isolate was isolated from human or animal. For example, high adhesion ability was observed for strain UCN 34 isolated from an infective endocarditis patient, whereas strain DSM 16831 isolated from koala feces adhered only marginally to collagen. Full genome microarray analysis of these two strains revealed strain-dependent gene expression due to adhesion. The expression of 25 genes of a transposon and 15 genes of a phage region in strain DSM 16831 were increased, which corresponds to horizontal gene transfer. Adherence to collagen in strain UCN 34 led to higher expression of 27 genes and lower expression of 31 genes. This was suggestive of a change in nutrient uptake.

Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential

There is a need to clarify relationships within the actinobacterial genus Micromonospora, the type genus of the family Micromonosporaceae, given its biotechnological and ecological importance. Here, draft genomes of 40 Micromonospora type strains and two non-type strains are made available through the Genomic Encyclopedia of Bacteria and Archaea project and used to generate a phylogenomic tree which showed they could be assigned to well supported phyletic lines that were not evident in corresponding trees based on single and concatenated sequences of conserved genes. DNA G+C ratios derived from genome sequences showed that corresponding data from species descriptions were imprecise. Emended descriptions include precise base composition data and approximate genome sizes of the type strains. antiSMASH analyses of the draft genomes show that micromonosporae have a previously unrealised potential to synthesize novel specialized metabolites. Close to one thousand biosynthetic gene clusters were detected, including NRPS, PKS, terpenes and siderophores clusters that were discontinuously distributed thereby opening up the prospect of prioritising gifted strains for natural product discovery. The distribution of key stress related genes provide an insight into how micromonosporae adapt to key environmental variables. Genes associated with plant interactions highlight the potential use of micromonosporae in agriculture and biotechnology.

Ribosome profiling reveals an adaptation strategy of reduced bacterium to acute stress

Bacteria of class Mollicutes (mycoplasmas) feature significant genome reduction which makes them good model organisms for systems biology studies. Previously we demonstrated, that drastic transcriptional response of mycoplasmas to stress results in a very limited response on the level of protein. In this study we used heat stress model of M. gallisepticum and ribosome profiling to elucidate the process of genetic information transfer under stress. We found that under heat stress ribosomes demonstrate selectivity towards mRNA binding. We identified that heat stress response may be divided into two groups on the basis of absolute transcript abundance and fold-change in the translatome. One represents a noise-like response and another is likely an adaptive one. The latter include ClpB chaperone, cell division cluster, homologs of immunoblocking proteins and short ORFs with unknown function. We found that previously identified read-through of terminators contributes to the upregulation of transcripts in the translatome as well. In addition we identified that ribosomes of M. gallisepticum undergo reorganization under the heat stress. The most notable event is decrease of the amount of associated HU protein. In conclusion, only changes of few adaptive transcripts significantly impact translatome, while widespread noise-like transcription plays insignificant role in translation during stress.

Global transcriptome analysis of the heat shock response of the deep-sea bacterium Shewanella piezotolerans WP3

For microorganisms, heat shock is a major stressful condition. Heat shock is characterized by sudden temperature increases that damage important protein structures and interfere with essential cellular functions. In this study, global gene expression patterns of the deep-sea bacterium Shewanella piezotolerans WP3 in response to heat shock were studied by DNA microarray analysis. Overall, 438, 573, and 627 genes were found to be differentially expressed after heat shock for 30, 60, and 90min, respectively. Functional classification of differentially transcribed genes was performed using the Clusters of Orthologous Groups of Proteins database. Additionally, 361 genes were identified as common differentially expressed genes. These genes may comprise the core genes responsible for coping with heat shock stress of WP3. Moreover, comparative analysis of gene expression pattern in WP3 and other bacteria indicated the presence of different adaptive strategies. These data represent the first transcriptome resource for the response of this deep-sea bacterium to high-temperature stress. This study contributes to the understanding of the global adaptation mechanisms of benthic bacteria toward environmental stresses.

The roles of RelA/(p)ppGpp in glucose-starvation induced adaptive response in the zoonotic Streptococcus suis

The (p)ppGpp signal molecules play a central role in the stringent response (SR) to adapt to nutrient starvation in bacteria, yet the carbohydrate starvation induced adaptive response and the roles of SR in this response is not well characterized, especially in Gram-positives. Here, two (p)ppGpp synthetases RelA and RelQ are identified in Streptococcus suis, an important emerging zoonotic Gram-positive bacterium, while only RelA is functional under glucose starvation. To characterize the roles of RelA/(p)ppGpp in glucose starvation response in S. suis, the growth curves and transcriptional profiles were compared between the mutant strain ΔrelA [a (p)ppGpp⁰ strain under glucose starvation] and its parental strain SC-19 [(p)ppGpp⁺]. The results showed great difference between SC-19 and ΔrelA on adaptive responses when suffering glucose starvation, and demonstrated that RelA/(p)ppGpp plays important roles in adaptation to glucose starvation. Besides the classic SR including inhibition of growth and related macromolecular synthesis, the extended adaptive response also includes inhibited glycolysis, and carbon catabolite repression (CCR)-mediated carbohydrate-dependent metabolic switches. Collectively, the pheno- and genotypic characterization of the glucose starvation induced adaptive response in S. suis makes a great contribution to understanding better the mechanism of SR.

Comparative Transcriptome Analysis of Vibrio splendidus JZ6 Reveals the Mechanism of Its Pathogenicity at Low Temperatures

Yesso scallop-pathogenic Vibrio splendidus strain JZ6 was found to have the highest virulence at 10°C, while its pathogenicity was significantly reduced with increased temperature and completely incapacitated at 28°C. In the present study, comparative transcriptome analyses of JZ6 and another nonpathogenic V. splendidus strain, TZ19, were conducted at two crucial culture temperatures (10°C and 28°C) in order to determine the possible mechanism of temperature regulation of virulence. Comparisons among four libraries, constructed from JZ6 and TZ19 cultured at 10°C and 28°C (designated JZ6_10, JZ6_28, TZ19_10, and TZ19_28), revealed that 241 genes were possibly related to the increased virulence of JZ6 at 10°C. There were 10 genes, including 2 encoding Flp pilus assembly proteins (FlhG and VS_2437), 6 encoding proteins of the "Vibrio cholerae pathogenic cycle" (ToxS, CqsA, CqsS, RpoS, HapR, and Vsm), and 2 encoding proteins in the Sec-dependent pathway (SecE and FtsY), that were significantly upregulated in JZ6_10 (P < 0.05) compared to those in JZ6_28, TZ19_10, and TZ19_28, which were supposed to be responsible for adhesion, quorum sensing, virulence, and protein secretion of V. splendidus. When cultured at 10°C, JZ6 cells were larger and tended to aggregate more than those cultured at 28°C. The virulence factor (extracellular metalloprotease) was also found to be highly expressed in the extracellular product (ECP) of JZ6 at 10°C, and this ECP exhibited obvious cytotoxicity to oyster primary hemocytes, A549 cells, and L929 cells. These results indicated that low temperatures (10°C) could enhance adhesion, activate the quorum sensing systems, upregulate virulence factor synthesis and secretion, and, lastly, increase the pathogenicity of JZ6.

Profiling of Brevibacillus borstelensis transcriptome exposed to high temperature shock

To understand the molecular mechanisms underlying the ability of the bacteria to survive at high temperature, gene expression profile of Brevibacillusborstelensis at 55°C during 5 and 10min heat shock period was carried out by high-throughput sequencing technology. A total of 2555 non-redundant transcripts were annotated. A total of 575 genes at 5min and 400 genes at 10min exhibited significant differential expression in response to temperature upshift from 50 to 55°C. Genes up-regulated under heat shock were associated with metabolism (mtnE), membrane transport, signal transduction, transcriptional regulation (ycxD, codY) and folding and sorting (hsp90). A larger number of genes encoding hypothetical proteins were identified. RT-PCR experimental results carried out on genes expressed under heat shock were found to be consistent with transcriptome data. The results enhance our understanding of adaptation strategy of thermophilic bacteria thereby providing a strong background for in depth research in thermophiles.

Identification of an archaeal mercury regulon by chromatin immunoprecipitation

Mercury is a heavy metal and toxic to all forms of life. Metal exposure can invoke a response to improve survival. In archaea, several components of a mercury response system have been identified, but it is not known whether metal transport is a member of this system. To identify such missing components, a peptide-tagged MerR transcription factor was used to localize enriched chromosome regions by chromosome immunoprecipitation combined with DNA sequence analysis. Such regions could serve as secondary regulatory binding sites to control the expression of additional genes associated with mercury detoxification. Among the 31 highly enriched loci, a subset of five was pursued as potential candidates based on their current annotations. Quantitative reverse transcription-PCR analysis of these regions with and without mercury treatment in WT and mutant strains lacking merR indicated significant regulatory responses under these conditions. Of these, a Family 5 extracellular solute-binding protein and the MarR transcription factor shown previously to control responses to oxidation were most strongly affected. Inactivation of the solute-binding protein by gene disruption increased the resistance of mutant cells to mercury challenge. Inductively coupled plasma-MS analysis of the mutant cell line following metal challenge indicated there was less intracellular mercury compared with the isogenic WT strain. Together, these regulated genes comprise new members of the archaeal MerR regulon and reveal a cascade of transcriptional control not previously demonstrated in this model organism.

Hydrogen peroxide induces adaptive response and differential gene expression in human embryo lung fibroblast cells

Hydrogen peroxide (H2 O2 ), a substance involved in cellular oxidative stress, has been observed to induce an adaptive response, which is characterized by a protection against the toxic effect of H2 O2 at higher concentrations. However, the molecular mechanism for the adaptive response remains unclear. In particular, the existing reports on H2 O2 -induced adaptive response are limited to animal cells and human tumor cells, and relatively normal human cells have never been observed for an adaptive response to H2 O2 . In this study, a human embryo lung fibroblast (MRC-5) cell line was used to model an adaptive response to H2 O2 , and the relevant differential gene expressions by using fluoro mRNA differential display RT-PCR. The results showed significant suppression of cytotoxicity of H2 O2 (1100 μM, 1 h) after pretreatment of the cells with H2 O2 at lower concentrations (0.088-8.8 μM, 24 h), as indicated by cell survival, lactate dehydrogenase release, and the rate of apoptotic cells. Totally 60 mRNA components were differentially expressed compared to untreated cells, and five of them (sizing 400-600 bp) which demonstrated the greatest increase in expression were cloned and sequenced. They showed identity with known genes, such as BCL-2, eIF3S5, NDUFS4, and RPS10. Real time RT-PCR analysis of the five genes displayed a pattern of differential expression consistent with that by the last method. These five genes may be involved in the induction of adaptive response by H2 O2 in human cells, at least in this particular cell type.

Evolution of microbiological analytical methods for dairy industry needs

Traditionally, culture-based methods have been used to enumerate microbial populations in dairy products. Recent developments in molecular methods now enable faster and more sensitive analyses than classical microbiology procedures. These molecular tools allow a detailed characterization of cell physiological states and bacterial fitness and thus, offer new perspectives to integration of microbial physiology monitoring to improve industrial processes. This review summarizes the methods described to enumerate and characterize physiological states of technological microbiota in dairy products, and discusses the current deficiencies in relation to the industry’s needs. Recent studies show that Polymerase chain reaction-based methods can successfully be applied to quantify fermenting microbes and probiotics in dairy products. Flow cytometry and omics technologies also show interesting analytical potentialities. However, they still suffer from a lack of validation and standardization for quality control analyses, as reflected by the absence of performance studies and official international standards.

Global transcriptional response to heat shock of the legume symbiont Mesorhizobium loti MAFF303099 comprises extensive gene downregulation

Rhizobia, the bacterial legume symbionts able to fix atmospheric nitrogen inside root nodules, have to survive in varied environmental conditions. The aim of this study was to analyse the transcriptional response to heat shock of Mesorhizobium loti MAFF303099, a rhizobium with a large multipartite genome of 7.6 Mb that nodulates the model legume Lotus japonicus. Using microarray analysis, extensive transcriptomic changes were detected in response to heat shock: 30% of the protein-coding genes were differentially expressed (2067 genes in the chromosome, 62 in pMLa and 57 in pMLb). The highest-induced genes are in the same operon and code for two sHSP. Only one of the five groEL genes in MAFF303099 genome was induced by heat shock. Unlike other prokaryotes, the transcriptional response of this Mesorhizobium included the underexpression of an unusually large number of genes (72% of the differentially expressed genes). This extensive downregulation of gene expression may be an important part of the heat shock response, as a way of reducing energetic costs under stress. To our knowledge, this study reports the heat shock response of the largest prokaryote genome analysed so far, representing an important contribution to understand the response of plant-interacting bacteria to challenging environmental conditions.

Global transcriptome analysis of Lactococcus garvieae strains in response to temperature

Lactococcus garvieae is an important fish and an opportunistic human pathogen. The genomic sequences of several L. garvieae strains have been recently published, opening the possibility of global studies on the biology of this pathogen. In this study, a whole genome DNA microarray of two strains of L. garvieae was designed and validated. This DNA microarray was used to investigate the effects of growth temperature (18°C and 37°C) on the transcriptome of two clinical strains of L. garvieae that were isolated from fish (Lg8831) and from a human case of septicemia (Lg21881). The transcriptome profiles evidenced a strain-specific response to temperature, which was more evident at 18°C. Among the most significant findings, Lg8831 was found to up-regulate at 18°C several genes encoding different cold-shock and cold-induced proteins involved in an efficient adaptive response of this strain to low-temperature conditions. Another relevant result was the description, for the first time, of respiratory metabolism in L. garvieae, whose gene expression regulation was temperature-dependent in Lg21881. This study provides new insights about how environmental factors such as temperature can affect L. garvieae gene expression. These data could improve our understanding of the regulatory networks and adaptive biology of this important pathogen.

Quantitative proteomics reveals the temperature-dependent proteins encoded by a series of cluster genes in thermoanaerobacter tengcongensis

Comprehensive and quantitative information of the thermophile proteome is an important source for understanding of the survival mechanism under high growth temperature. Thermoanaerobacter tengcongensis (T. tengcongensis), a typical anaerobic thermophilic eubacterium, was selected to quantitatively evaluate its protein abundance changes in response to four different temperatures. With optimized procedures of isobaric tags for relative and absolute quantitation quantitative proteomics (iTRAQ), such as peptide fractionation with high-pH reverse phase (RP) high performance liquid chromatography (HPLC), tandem MS acquisition mode in LTQ Orbitrap Velos MS, and evaluation of the quantification algorithms, high quality of the quantitative information of the peptides identified were acquired. In total, 1589 unique proteins were identified and defined 251 as the temperature-dependent proteins. Analysis of genomic locations toward the correspondent genes of these temperature-dependent proteins revealed that more than 30% were contiguous units with relevant biological functions, which are likely to form the operon structures in T. tengcongensis. The RNA sequencing (RNA-seq) data further demonstrated that these cluster genes were cotranscribed, and their mRNA abundance changes responding to temperature exhibited the similar trends as the proteomic results, suggesting that the temperature-dependent proteins are highly associated with the correspondent transcription status. Hence, the operon regulation is likely an energy-efficient mode for T. tengcongensis survival. In addition, evaluation to the functions of differential proteomes indicated that the abundance of the proteins participating in sulfur-respiration on the plasma membrane was decreased as the temperature increased, whereas the glycolysis-related protein abundance was increased. The energy supply in T. tengcongensis at high temperature is, therefore, speculated not mainly through the respiration chain reactions.