scholarly journals Transcriptomic Analysis of Temperature Responses of Aspergillus kawachii during Barley Koji Production

2014 ◽  
Vol 81 (4) ◽  
pp. 1353-1363 ◽  
Author(s):  
Taiki Futagami ◽  
Kazuki Mori ◽  
Shotaro Wada ◽  
Hiroko Ida ◽  
Yasuhiro Kajiwara ◽  
...  
Keyword(s):  
Gene Expression ◽  
Citric Acid ◽  
Solid State ◽  
Pentose Phosphate ◽  
Temperature Modulation ◽  
Cultivation Temperature ◽  
Content Type ◽  
Expression Of Genes ◽  
Aspergillus Kawachii ◽  
Heat Shock Responses

ABSTRACTThe koji moldAspergillus kawachiiis used for making the Japanese distilled spirit shochu. During shochu production,A. kawachiiis grown in solid-state culture (koji) on steamed grains, such as rice or barley, to convert the grain starch to glucose and produce citric acid. During this process, the cultivation temperature ofA. kawachiiis gradually increased to 40°C and is then lowered to 30°C. This temperature modulation is important for stimulating amylase activity and the accumulation of citric acid. However, the effects of temperature onA. kawachiiat the gene expression level have not been elucidated. In this study, we investigated the effect of solid-state cultivation temperature on gene expression forA. kawachiigrown on barley. The results of DNA microarray and gene ontology analyses showed that the expression of genes involved in the glycerol, trehalose, and pentose phosphate metabolic pathways, which function downstream of glycolysis, was downregulated by shifting the cultivation temperature from 40 to 30°C. In addition, significantly reduced expression of genes related to heat shock responses and increased expression of genes related with amino acid transport were also observed. These results suggest that solid-state cultivation at 40°C is stressful forA. kawachiiand that heat adaptation leads to reduced citric acid accumulation through activation of pathways branching from glycolysis. The gene expression profile ofA. kawachiielucidated in this study is expected to contribute to the understanding of gene regulation during koji production and optimization of the industrially desirable characteristics ofA. kawachii.

scholarly journals Peripheral Insulin Regulates a Broad Network of Gene Expression in the Hypothalamus, Hippocampus and Nucleus Accumbens

2021 ◽  
Author(s):  
Weikang Cai ◽  
Xuemei Zhang ◽  
Thiago M. Batista ◽  
Rubén García-Martín ◽  
Samir Softic ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nucleus Accumbens ◽  
Cholesterol Biosynthesis ◽  
Peripheral Circulation ◽  
Fatty Acyl ◽  
Pentose Phosphate ◽  
Gaba A ◽  
Expression Of Genes ◽  
Pentose Phosphate Pathways ◽  
The Brain

The brain is now recognized as an insulin sensitive tissue, however, the role of changing insulin concentrations in the peripheral circulation on gene expression in the brain is largely unknown. Here we perform hyperinsulinemic-euglycemic clamp on 3-month-old male C57BL/6 mice for 3 hours. We show that increases in peripheral insulin within the physiological range regulate expression of a broad network of gene expression in the brain compared with saline-infused controls. Insulin regulates distinct pathways in the hypothalamus, hippocampus and nucleus accumbens. Insulin shows its most robust effect in the hypothalamus and regulates multiple genes involved in neurotransmission, including up-regulating expression of multiple subunits of GABA-A receptors, Na<sup>+</sup> and K<sup>+</sup> channels, and SNARE proteins; differentially modulating glutamate receptors; and suppressing multiple neuropeptides. Insulin also strongly modulates metabolic genes in the hypothalamus, suppressing genes in the glycolysis and pentose phosphate pathways, while increasing expression of genes regulating pyruvate dehydrogenase and long-chain fatty acyl-CoA and cholesterol biosynthesis, thereby rerouting of carbon substrates from glucose metabolism to lipid metabolism required for the biogenesis of membranes for neuronal and glial function and synaptic remodeling. Furthermore, based on the transcriptional signatures, these changes in gene expression involve neurons, astrocytes, oligodendrocytes, microglia and endothelial cells. Thus, peripheral insulin acutely and potently regulates expression of a broad network of genes involved in neurotransmission and brain metabolism. Dysregulation of these pathways could have dramatic effects in normal physiology and diabetes.

scholarly journals Transcription Factor Atf1 Regulates Expression of Cellulase and Xylanase Genes during Solid-State Fermentation of Ascomycetes

2019 ◽  
Vol 85 (24) ◽  
Author(s):  
Shuai Zhao ◽  
Xu-Zhong Liao ◽  
Jiu-Xiang Wang ◽  
Yuan-Ni Ning ◽  
Cheng-Xi Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Solid State ◽  
Rna Sequencing ◽  
Solid State Fermentation ◽  
Carbon Sources ◽  
Penicillium Oxalicum ◽  
Xylanase Production ◽  
Content Type ◽  
Ascomycete Fungi

ABSTRACT Transcriptional regulation of cellulolytic and xylolytic genes in ascomycete fungi is controlled by specific carbon sources in different external environments. Here, comparative transcriptomic analyses of Penicillium oxalicum grown on wheat bran (WB), WB plus rice straw (WR), or WB plus Avicel (WA) as the sole carbon source under solid-state fermentation (SSF) revealed that most of the differentially expressed genes (DEGs) were involved in metabolism, specifically, carbohydrate metabolism. Of the DEGs, the basic core carbohydrate-active enzyme-encoding genes which responded to the plant biomass resources were identified in P. oxalicum, and their transcriptional levels changed to various extents depending on the different carbon sources. Moreover, this study found that three deletion mutants of genes encoding putative transcription factors showed significant alterations in filter paper cellulase production compared with that of a parental P. oxalicum strain with a deletion of Ku70 (ΔPoxKu70 strain) when grown on WR under SSF. Importantly, the ΔPoxAtf1 mutant (with a deletion of P. oxalicum Atf1, also called POX03016) displayed 46.1 to 183.2% more cellulase and xylanase production than a ΔPoxKu70 mutant after 2 days of growth on WR. RNA sequencing and quantitative reverse transcription-PCR revealed that PoxAtf1 dynamically regulated the expression of major cellulase and xylanase genes under SSF. PoxAtf1 bound to the promoter regions of the key cellulase and xylanase genes in vitro. This study provides novel insights into the regulatory mechanism of fungal cellulase and xylanase gene expression under SSF. IMPORTANCE The transition to a more environmentally friendly economy encourages studies involving the high-value-added utilization of lignocellulosic biomass. Solid-state fermentation (SSF), that simulates the natural habitat of soil microorganisms, is used for a variety of applications such as biomass biorefinery. Prior to the current study, our understanding of genome-wide gene expression and of the regulation of gene expression of lignocellulose-degrading enzymes in ascomycete fungi during SSF was limited. Here, we employed RNA sequencing and genetic analyses to investigate transcriptomes of Penicillium oxalicum strain EU2101 cultured on medium containing different carbon sources and to identify and characterize transcription factors for regulating the expression of cellulase and xylanase genes during SSF. The results generated will provide novel insights into genetic engineering of filamentous fungi to further increase enzyme production.

scholarly journals Chitin-Induced Gene Expression in Secondary Metabolic Pathways of Streptomyces coelicolor A3(2) Grown in Soil

2012 ◽  
Vol 79 (2) ◽  
pp. 707-713 ◽  
Author(s):  
Behnam Nazari ◽  
Michihiko Kobayashi ◽  
Akihiro Saito ◽  
Azam Hassaninasab ◽  
Kiyotaka Miyashita ◽  
...  
Keyword(s):  
Gene Expression ◽  
Secondary Metabolism ◽  
Stress Responses ◽  
Metabolic Pathways ◽  
Streptomyces Coelicolor ◽  
Regulation Of Gene Expression ◽  
Content Type ◽  
Metabolic Genes ◽  
Expression Of Genes ◽  
Microarray Analyses

ABSTRACTMicroarray analyses revealed that the expression of genes for secondary metabolism together with that of primary metabolic genes was induced by chitin in autoclaved soil cultures ofStreptomyces coelicolorA3(2). The data also indicated that DasR was involved in the regulation of gene expression for chitin catabolism, secondary metabolism, and stress responses.

scholarly journals The Fatty Acid Regulator FadR Influences the Expression of the Virulence Cascade in the El Tor Biotype of Vibrio cholerae by Modulating the Levels of ToxT via Two Different Mechanisms

2017 ◽  
Vol 199 (7) ◽  
Author(s):  
Gabriela Kovacikova ◽  
Wei Lin ◽  
Ronald K. Taylor ◽  
Karen Skorupski
Keyword(s):  
Gene Expression ◽  
Vibrio Cholerae ◽  
Virulence Gene ◽  
Enteric Bacteria ◽  
Posttranslational Regulation ◽  
Content Type ◽  
Virulence Gene Expression ◽  
Expression Of Genes ◽  
El Tor ◽  
Virulence Regulator

ABSTRACT FadR is a master regulator of fatty acid (FA) metabolism that coordinates the pathways of FA degradation and biosynthesis in enteric bacteria. We show here that a ΔfadR mutation in the El Tor biotype of Vibrio cholerae prevents the expression of the virulence cascade by influencing both the transcription and the posttranslational regulation of the master virulence regulator ToxT. FadR is a transcriptional regulator that represses the expression of genes involved in FA degradation, activates the expression of genes involved in unsaturated FA (UFA) biosynthesis, and also activates the expression of two operons involved in saturated FA (SFA) biosynthesis. Since FadR does not bind directly to the toxT promoter, we determined whether the regulation of any of its target genes indirectly influenced ToxT. This was accomplished by individually inserting a double point mutation into the FadR-binding site in the promoter of each target gene, thereby preventing their activation or repression. Although preventing FadR-mediated activation of fabA, which encodes the enzyme that carries out the first step in UFA biosynthesis, did not significantly influence either the transcription or the translation of ToxT, it reduced its levels and prevented virulence gene expression. In the mutant strain unable to carry out FadR-mediated activation of fabA, expressing fabA ectopically restored the levels of ToxT and virulence gene expression. Taken together, the results presented here indicate that V. cholerae FadR influences the virulence cascade in the El Tor biotype by modulating the levels of ToxT via two different mechanisms. IMPORTANCE Fatty acids (FAs) play important roles in membrane lipid homeostasis and energy metabolism in all organisms. In Vibrio cholerae, the causative agent of the acute intestinal disease cholera, they also influence virulence by binding into an N-terminal pocket of the master virulence regulator, ToxT, and modulating its activity. FadR is a transcription factor that coordinately controls the pathways of FA degradation and biosynthesis in enteric bacteria. This study identifies a new link between FA metabolism and virulence in the El Tor biotype by showing that FadR influences both the transcription and posttranslational regulation of the master virulence regulator ToxT by two distinct mechanisms.

scholarly journals Expression of genes involved in key metabolic processes during winter flounder (Pseudopleuronectes americanus) metamorphosis

2013 ◽  
Vol 91 (3) ◽  
pp. 156-163 ◽  
Author(s):  
Marie Vagner ◽  
Benjamin de Montgolfier ◽  
Jean-Marie Sévigny ◽  
Réjean Tremblay ◽  
Céline Audet
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Pentose Phosphate ◽  
Winter Flounder ◽  
Benthic Habitat ◽  
Pseudopleuronectes Americanus ◽  
Metabolic Processes ◽  
Expression Of Genes ◽  
Molecular Events ◽  
Gh Gene

The aim of this study was to better understand the molecular events governing ontogeny in winter flounder (Pseudopleuronectes americanus (Walbaum, 1792)). The expression of seven genes involved in key metabolic processes during metamorphosis were measured at settlement (S0), at 15 (S15), and 30 (S30) days after settlement and compared with those in pelagic larvae prior to settlement (PL). Two critical stages were identified: (1) larval transit from the pelagic to the benthic habitat (from PL to S0) and (2) metamorphosis maturation, when the larvae stay settled without growth (from S0 to S30). Growth hormone (gh) gene expression significantly increased at S0. At S30, an increase in cytochrome oxidase (cox) gene expression occurred with a second surge of gh gene expression, suggesting that enhanced aerobic capacity was supporting growth before the temperature decrease in the fall. Expression patterns of pyruvate kinase (pk), glucose-6-phosphate dehydrogenase (g6pd), and bile salt activated lipase (bal) genes indicated that energy synthesis may be mainly supplied through glycolysis in PL, through the pentose–phosphate pathway at settlement, and through lipid metabolism at S30. The expression of the heat-shock protein 70 (hsp70), superoxide dismutase (sod), cox, and peroxiredoxin-6 (prx6) genes revealed that oxidative stress and the consequent development of antioxidative protection were limited during the PL stage, reinforced at settlement, and very high at S30, certainly owing to the higher growth rate observed at this period.

scholarly journals Genome Sequence of the White Koji Mold Aspergillus kawachii IFO 4308, Used for Brewing the Japanese Distilled Spirit Shochu

2011 ◽  
Vol 10 (11) ◽  
pp. 1586-1587 ◽  
Author(s):  
Taiki Futagami ◽  
Kazuki Mori ◽  
Ayaka Yamashita ◽  
Shotaro Wada ◽  
Yasuhiro Kajiwara ◽  
...  
Keyword(s):  
Citric Acid ◽  
Genome Sequence ◽  
Filamentous Fungus ◽  
Industrial Applications ◽  
Glycoside Hydrolases ◽  
Content Type ◽  
Aspergillus Kawachii ◽  
Koji Mold ◽  
Further Development ◽  
Insight Into

ABSTRACT The filamentous fungus Aspergillus kawachii has traditionally been used for brewing the Japanese distilled spirit shochu. A. kawachii characteristically hyperproduces citric acid and a variety of polysaccharide glycoside hydrolases. Here the genome sequence of A. kawachii IFO 4308 was determined and annotated. Analysis of the sequence may provide insight into the properties of this fungus that make it superior for use in shochu production, leading to the further development of A. kawachii for industrial applications.

scholarly journals Peripheral Insulin Regulates a Broad Network of Gene Expression in the Hypothalamus, Hippocampus and Nucleus Accumbens

2021 ◽  
Author(s):  
Weikang Cai ◽  
Xuemei Zhang ◽  
Thiago M. Batista ◽  
Rubén García-Martín ◽  
Samir Softic ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nucleus Accumbens ◽  
Cholesterol Biosynthesis ◽  
Peripheral Circulation ◽  
Fatty Acyl ◽  
Pentose Phosphate ◽  
Gaba A ◽  
Expression Of Genes ◽  
Pentose Phosphate Pathways ◽  
The Brain

The brain is now recognized as an insulin sensitive tissue, however, the role of changing insulin concentrations in the peripheral circulation on gene expression in the brain is largely unknown. Here we perform hyperinsulinemic-euglycemic clamp on 3-month-old male C57BL/6 mice for 3 hours. We show that increases in peripheral insulin within the physiological range regulate expression of a broad network of gene expression in the brain compared with saline-infused controls. Insulin regulates distinct pathways in the hypothalamus, hippocampus and nucleus accumbens. Insulin shows its most robust effect in the hypothalamus and regulates multiple genes involved in neurotransmission, including up-regulating expression of multiple subunits of GABA-A receptors, Na<sup>+</sup> and K<sup>+</sup> channels, and SNARE proteins; differentially modulating glutamate receptors; and suppressing multiple neuropeptides. Insulin also strongly modulates metabolic genes in the hypothalamus, suppressing genes in the glycolysis and pentose phosphate pathways, while increasing expression of genes regulating pyruvate dehydrogenase and long-chain fatty acyl-CoA and cholesterol biosynthesis, thereby rerouting of carbon substrates from glucose metabolism to lipid metabolism required for the biogenesis of membranes for neuronal and glial function and synaptic remodeling. Furthermore, based on the transcriptional signatures, these changes in gene expression involve neurons, astrocytes, oligodendrocytes, microglia and endothelial cells. Thus, peripheral insulin acutely and potently regulates expression of a broad network of genes involved in neurotransmission and brain metabolism. Dysregulation of these pathways could have dramatic effects in normal physiology and diabetes.

scholarly journals Impact of Anaerobiosis on Expression of the Iron-Responsive Fur and RyhB Regulons

mBio ◽  
2015 ◽  
Vol 6 (6) ◽  
Author(s):  
Nicole A. Beauchene ◽  
Kevin S. Myers ◽  
Dongjun Chung ◽  
Dan M. Park ◽  
Allison M. Weisnicht ◽  
...  
Keyword(s):  
Gene Expression ◽  
Small Rna ◽  
Iron Homeostasis ◽  
Target Genes ◽  
Arms Race ◽  
Anaerobic Conditions ◽  
Content Type ◽  
Expression Of Genes ◽  
Aerobic And Anaerobic ◽  
Aerobic And Anaerobic Conditions

ABSTRACTIron, a major protein cofactor, is essential for most organisms. Despite the well-known effects of O2on the oxidation state and solubility of iron, the impact of O2on cellular iron homeostasis is not well understood. Here we report that inEscherichia coliK-12, the lack of O2dramatically changes expression of genes controlled by the global regulators of iron homeostasis, the transcription factor Fur and the small RNA RyhB. Using chromatin immunoprecipitation sequencing (ChIP-seq), we found anaerobic conditions promote Fur binding to more locations across the genome. However, by expression profiling, we discovered that the major effect of anaerobiosis was to increase the magnitude of Fur regulation, leading to increased expression of iron storage proteins and decreased expression of most iron uptake pathways and several Mn-binding proteins. This change in the pattern of gene expression also correlated with an unanticipated decrease in Mn in anaerobic cells. Changes in the genes posttranscriptionally regulated by RyhB under aerobic and anaerobic conditions could be attributed to O2-dependent changes in transcription of the target genes: aerobic RyhB targets were enriched in iron-containing proteins associated with aerobic energy metabolism, whereas anaerobic RyhB targets were enriched in iron-containing anaerobic respiratory functions. Overall, these studies showed that anaerobiosis has a larger impact on iron homeostasis than previously anticipated, both by expanding the number of direct Fur target genes and the magnitude of their regulation and by altering the expression of genes predicted to be posttranscriptionally regulated by the small RNA RyhB under iron-limiting conditions.IMPORTANCEMicrobes and host cells engage in an “arms race” for iron, an essential nutrient that is often scarce in the environment. Studies of iron homeostasis have been key to understanding the control of iron acquisition and the downstream pathways that enable microbes to compete for this valuable resource. Here we report that O2availability affects the gene expression programs of twoEscherichia colimaster regulators that function in iron homeostasis: the transcription factor Fur and the small RNA regulator RyhB. Fur appeared to be more active under anaerobic conditions, suggesting a change in the set point for iron homeostasis. RyhB preferentially targeted iron-containing proteins of respiration-linked pathways, which are differentially expressed under aerobic and anaerobic conditions. Such findings may be relevant to the success of bacteria within their hosts since zones of reduced O2may actually reduce bacterial iron demands, making it easier to win the arms race for iron.

scholarly journals Modulation of Chicken Intestinal Immune Gene Expression by Small Cationic Peptides as Feed Additives during the First Week Posthatch

2013 ◽  
Vol 20 (9) ◽  
pp. 1440-1448 ◽  
Author(s):  
Michael H. Kogut ◽  
Kenneth J. Genovese ◽  
Haiqi He ◽  
Christina L. Swaggerty ◽  
Yiwei Jiang
Keyword(s):  
Gene Expression ◽  
Proinflammatory Cytokines ◽  
Proinflammatory Cytokine ◽  
Feed Additives ◽  
Feed Additive ◽  
Cationic Peptides ◽  
Type I ◽  
Immune Gene ◽  
Content Type ◽  
Functional Efficiency

ABSTRACTWe have been investigating modulation strategies tailored around the selective stimulation of the host's immune system as an alternative to direct targeting of microbial pathogens by antibiotics. One such approach is the use of a group of small cationic peptides (BT) produced by a Gram-positive soil bacterium,Brevibacillus texasporus. These peptides have immune modulatory properties that enhance both leukocyte functional efficiency and leukocyte proinflammatory cytokine and chemokine mRNA transcription activitiesin vitro. In addition, when provided as a feed additive for just 4 days posthatch, BT peptides significantly induce a concentration-dependent protection against cecal and extraintestinal colonization bySalmonella entericaserovar Enteritidis. In the present studies, we assessed the effects of feeding BT peptides on transcriptional changes on proinflammatory cytokines, inflammatory chemokines, and Toll-like receptors (TLR) in the ceca of broiler chickens with and withoutS. Enteritidis infection. After feeding a BT peptide-supplemented diet for the first 4 days posthatch, chickens were then challenged withS. Enteritidis, and intestinal gene expression was measured at 1 or 7 days postinfection (p.i.) (5 or 11 days of age). Intestinal expression of innate immune mRNA transcripts was analyzed by quantitative real-time PCR (qRT-PCR). Analysis of relative mRNA expression showed that a BT peptide-supplemented diet did not directly induce the transcription of proinflammatory cytokine, inflammatory chemokine, type I/II interferon (IFN), or TLR mRNA in chicken cecum. However, feeding the BT peptide-supplemented diet primed cecal tissue for increased (P≤ 0.05) transcription of TLR4, TLR15, and TLR21 upon infection withS. Enteritidis on days 1 and 7 p.i. Likewise, feeding the BT peptides primed the cecal tissue for increased transcription of proinflammatory cytokines (interleukin 1β [IL-1β], IL-6, IL-18, type I and II IFNs) and inflammatory chemokine (CxCLi2) in response toS. Enteritidis infection 1 and 7 days p.i. compared to the chickens fed the basal diet. These small cationic peptides may prove useful as alternatives to antibiotics as local immune modulators in neonatal poultry by providing prophylactic protection againstSalmonellainfections.

scholarly journals Cinnamon Oil Inhibits Penicillium expansum Growth by Disturbing the Carbohydrate Metabolic Process

2021 ◽  
Vol 7 (2) ◽  
pp. 123
Author(s):  
Tongfei Lai ◽  
Yangying Sun ◽  
Yaoyao Liu ◽  
Ran Li ◽  
Yuanzhi Chen ◽  
...  
Keyword(s):  
Pentose Phosphate ◽  
Metabolic Process ◽  
Penicillium Expansum ◽  
Economic Losses ◽  
Pome Fruit ◽  
Cinnamon Oil ◽  
Atp Production ◽  
Protein Levels ◽  
Regulatory Enzymes ◽  
Expression Of Genes

Penicillium expansum is a major postharvest pathogen that mainly threatens the global pome fruit industry and causes great economic losses annually. In the present study, the antifungal effects and potential mechanism of cinnamon oil against P. expansum were investigated. Results indicated that 0.25 mg L−1 cinnamon oil could efficiently inhibit the spore germination, conidial production, mycelial accumulation, and expansion of P. expansum. In addition, it could effectively control blue mold rots induced by P. expansum in apples. Cinnamon oil could also reduce the expression of genes involved in patulin biosynthesis. Through a proteomic quantitative analysis, a total of 146 differentially expressed proteins (DEPs) involved in the carbohydrate metabolic process, most of which were down-regulated, were noticed for their large number and functional significance. Meanwhile, the expressions of 14 candidate genes corresponding to DEPs and the activities of six key regulatory enzymes (involving in cellulose hydrolyzation, Krebs circle, glycolysis, and pentose phosphate pathway) showed a similar trend in protein levels. In addition, extracellular carbohydrate consumption, intracellular carbohydrate accumulation, and ATP production of P. expansum under cinnamon oil stress were significantly decreased. Basing on the correlated and mutually authenticated results, we speculated that disturbing the fungal carbohydrate metabolic process would be partly responsible for the inhibitory effects of cinnamon oil on P. expansum growth. The findings would provide new insights into the antimicrobial mode of cinnamon oil.

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