Gene expression analysis of Alcaligenes faecalis during induction of heterotrophic nitrification

AbstractAlcaligenes faecalis is a heterotrophic nitrifying bacterium that oxidizes ammonia and generates nitrite and nitrate. When A. faecalis was cultivated in a medium containing pyruvate and ammonia as the sole carbon and nitrogen sources, respectively, high concentrations of nitrite accumulated in the medium whose carbon/nitrogen (C/N) ratio was lower than 10 during the exponential growth phase, while the accumulation was not observed in the medium whose C/N ratio was higher than 15. Comparative transcriptome analysis was performed using nitrifying and non-nitrifying cells of A. faecalis cultivated in media whose C/N ratios were 5 and 20, respectively, to evaluate the fluctuations of gene expression during induction of heterotrophic nitrification. Expression levels of genes involved in primary metabolism did not change significantly in the cells at the exponential growth phase under both conditions. We observed a significant increase in the expression levels of four gene clusters: pod cluster containing the gene encoding pyruvic oxime dioxygenase (POD), podh cluster containing the gene encoding a POD homolog (PODh), suf cluster involved in an iron-sulfur cluster biogenesis, and dnf cluster involved in a novel hydroxylamine oxidation pathway in the nitrifying cells. Our results provide valuable insight into the biochemical mechanism of heterotrophic nitrification.

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Global gene expression analysis of Streptococcus agalactiae at exponential growth phase

10.1101/2020.11.13.381939 ◽

2020 ◽

Author(s):

Inês Silvestre ◽

Vítor Borges ◽

Sílvia Duarte ◽

Alexandra Nunes ◽

Rita Sobral ◽

...

Keyword(s):

Gene Expression ◽

Growth Phase ◽

Exponential Growth ◽

Streptococcus Agalactiae ◽

Molecular Mechanisms ◽

Reference Strain ◽

Global Gene Expression ◽

Exponential Growth Phase ◽

Expression Levels

AbstractStreptococcus agalactiae is a leading cause of neonatal infections and an increasing cause of infections in adults with underlying diseases. One of the first S. agalactiae isolates to be subjected to whole genome sequencing was NEM316, a strain responsible for a fatal case of septicemia that has been widely used as reference strain for in vitro assays. Whole transcriptome analyses may provide an essential contribute to the understanding of the molecular mechanisms responsible for bacteria adaptation and pathogenicity, still, so far, very few studies were dedicated to the analysis of global gene expression of S. agalactiae. Here, we applied RNA-sequencing to perform a comparative overview of the global gene expression levels of the S. agalactiae reference strain NEM316 at the exponential growth phase. Genes were ranked by expression level and grouped by functional category and 46% of the top-100 expressed genes encode proteins involved in “Translation, ribosomal structure and biogenesis”. Among the group of highly expressed genes were also represented genes with no assigned functional category. Although this result warrants further investigation, most of them might be implicated in stress response. As very little is known about the molecular mechanisms behind the release of DNase’s in vitro and in vivo, we also performed preliminary assays to understand whether direct DNA exposure affects the gene expression of strain NEM316 at the exponential growth phase. No differentially expressed genes were detected, which indicates that follow-up studies are needed to disclose the complex molecular pathways (and stimuli) triggering the release of DNase’s. In general, we provide data on the global expression levels of NEM316 at exponential growth phase that may contribute to better understand S. agalactiae adaptation and virulence.

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Interplay of CodY and ScoC in the Regulation of Major Extracellular Protease Genes of Bacillus subtilis

Journal of Bacteriology ◽

10.1128/jb.00894-15 ◽

2016 ◽

Vol 198 (6) ◽

pp. 907-920 ◽

Cited By ~ 18

Author(s):

Giulia Barbieri ◽

Alessandra M. Albertini ◽

Eugenio Ferrari ◽

Abraham L. Sonenshein ◽

Boris R. Belitsky

Keyword(s):

Gene Expression ◽

Bacillus Subtilis ◽

Growth Phase ◽

Exponential Growth ◽

Degradation Products ◽

Transcriptional Regulator ◽

Complex Medium ◽

Exponential Growth Phase ◽

Content Type ◽

In Cells

ABSTRACTAprE and NprE are two major extracellular proteases inBacillus subtiliswhose expression is directly regulated by several pleiotropic transcriptional factors, including AbrB, DegU, ScoC, and SinR. In cells growing in a rich, complex medium, theaprEandnprEgenes are strongly expressed only during the post-exponential growth phase; mutations in genes encoding the known regulators affect the level of post-exponential-phase gene expression but do not permit high-level expression during the exponential growth phase. Using DNA-binding assays and expression and mutational analyses, we have shown that the genes for both exoproteases are also under strong, direct, negative control by the global transcriptional regulator CodY. However, because CodY also repressesscoC, little or no derepression ofaprEandnprEwas seen in acodYnull mutant due to overexpression ofscoC. Thus, CodY is also an indirect positive regulator of these genes by limiting the synthesis of a second repressor. In addition, in cells growing under conditions that activate CodY, ascoCnull mutation had little effect onaprEornprEexpression; full effects ofscoCorcodYnull mutations could be seen only in the absence of the other regulator. However, even thecodY scoCdouble mutant did not show high levels ofaprEandnprEgene expression during exponential growth phase in a rich, complex medium. Only a third mutation, inabrB, allowed such expression. Thus, three repressors can contribute to reducing exoprotease gene expression during growth in the presence of excess nutrients.IMPORTANCEThe majorBacillus subtilisexoproteases, AprE and NprE, are important metabolic enzymes whose genes are subject to complex regulation by multiple transcription factors. We show here that expression of theaprEandnprEgenes is also controlled, both directly and indirectly, by CodY, a global transcriptional regulator that responds to the intracellular pools of amino acids. Direct CodY-mediated repression explains a long-standing puzzle, that is, why exoproteases are not produced when cells are growing exponentially in a medium containing abundant quantities of proteins or their degradation products. Indirect regulation ofaprEandnprEthrough CodY-mediated repression of thescoCgene, encoding another pleiotropic repressor, serves to maintain a significant level of repression of exoprotease genes when CodY loses activity.

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Membrane protein structures enter an exponential growth phase

PSI Structural Genomics Knowledgebase ◽

10.1038/fa_sbkb.2010.39 ◽

2010 ◽

Author(s):

Michelle Montoya

Keyword(s):

Membrane Protein ◽

Growth Phase ◽

Exponential Growth ◽

Protein Structures ◽

Exponential Growth Phase

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Activation of the expression of the microcin C51 operon upon glucose starvation of cells at the exponential growth phase

Russian Journal of Genetics ◽

10.1007/s11177-005-0061-5 ◽

2005 ◽

Vol 41 (1) ◽

pp. 40-43

Author(s):

A. M. Veselovskii ◽

A. Z. Metlitskaya ◽

V. A. Lipasova ◽

I. A. Bass ◽

I. A. Khmel

Keyword(s):

Growth Phase ◽

Exponential Growth ◽

Exponential Growth Phase ◽

Glucose Starvation

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Differences in power-law growth over time and indicators of COVID-19 pandemic progression worldwide

10.1101/2020.03.31.20048827 ◽

2020 ◽

Cited By ~ 1

Author(s):

Jack Merrin

Keyword(s):

Error Analysis ◽

Real Time ◽

Power Law ◽

Growth Phase ◽

Exponential Growth ◽

Spreading Rate ◽

Exponential Growth Phase ◽

Power Law Exponent ◽

Disease Spreading ◽

Over Time

1AbstractAn automated statistical and error analysis of 45 countries or regions with more than 1000 cases of COVID-19 as of March 28, 2020, has been performed. This study reveals differences in the rate of disease spreading rate over time in different countries. This survey observes that most countries undergo a beginning exponential growth phase, which transitions into a power-law phase, as recently suggested by Ziff and Ziff. Tracking indicators of growth, such as the power-law exponent, are a good indication of the relative danger different countries are in and show when social measures are effective towards slowing the spread. The data compiled here are usefully synthesizing a global picture, identifying country to country variation in spreading, and identifying countries most at risk. This analysis may factor into how best to track the effectiveness of social distancing policies and quarantines in real-time as data is updated each day.

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Biosynthesis and turnover of outer-membrane proteins in Escherichia coli ML308-225

Biochemical Journal ◽

10.1042/bj1820407 ◽

1979 ◽

Vol 182 (2) ◽

pp. 407-412 ◽

Cited By ~ 3

Author(s):

R J Allen ◽

G K Scott

Keyword(s):

Escherichia Coli ◽

Protein Synthesis ◽

Outer Membrane ◽

Bacterial Growth ◽

Growth Phase ◽

Exponential Growth ◽

Outer Membrane Proteins ◽

Exponential Growth Phase ◽

Outer Membranes ◽

Dilution Experiments

Isolated outer membranes and outer-membrane extracts from Escherichia coli ML308-225 in the early-exponential growth phase contain more protein than do corresponding preparations from late-exponential- or stationary-phase bacteria. Isotope-dilution experiments show that this is due to a loss of protein from the membrane during the exponential growth phase. Inhibition of bacterial growth and protein synthesis stabilizes the outer-membrane-protein concentration. Protein synthesis in the absence of bacterial growth results in higher concentrations of protein in the outer membrane.

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Exponential growth phase ofPseudomonas methanolica batch cultures

Zeitschrift für allgemeine Mikrobiologie ◽

10.1002/jobm.3630130610 ◽

1973 ◽

Vol 13 (6) ◽

pp. 523-528 ◽

Cited By ~ 1

Author(s):

E. M. Shulgovskaya ◽

I. I. Ivanova ◽

G. G. Sotnicov

Keyword(s):

Growth Phase ◽

Exponential Growth ◽

Exponential Growth Phase ◽

Batch Cultures

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The Putrescine Importer PuuP of Escherichia coli K-12

Journal of Bacteriology ◽

10.1128/jb.01314-08 ◽

2009 ◽

Vol 191 (8) ◽

pp. 2776-2782 ◽

Cited By ~ 36

Author(s):

Shin Kurihara ◽

Yuichi Tsuboi ◽

Shinpei Oda ◽

Hyeon Guk Kim ◽

Hidehiko Kumagai ◽

...

Keyword(s):

Escherichia Coli ◽

Gene Cluster ◽

Growth Phase ◽

Exponential Growth ◽

Minimal Medium ◽

Exponential Growth Phase ◽

E Coli ◽

Genes Encoding ◽

K 12 ◽

Utilization Pathway

ABSTRACT The Puu pathway is a putrescine utilization pathway involving gamma-glutamyl intermediates. The genes encoding the enzymes of the Puu pathway form a gene cluster, the puu gene cluster, and puuP is one of the genes in this cluster. In Escherichia coli, three putrescine importers, PotFGHI, PotABCD, and PotE, were discovered in the 1990s and have been studied; however, PuuP had not been discovered previously. This paper shows that PuuP is a novel putrescine importer whose kinetic parameters are equivalent to those of the polyamine importers discovered previously. A puuP + strain absorbed up to 5 mM putrescine from the medium, but a ΔpuuP strain did not. E. coli strain MA261 has been used in previous studies of polyamine transporters, but PuuP had not been identified previously. It was revealed that the puuP gene of MA261 was inactivated by a point mutation. When E. coli was grown on minimal medium supplemented with putrescine as the sole carbon or nitrogen source, only PuuP among the polyamine importers was required. puuP was expressed strongly when putrescine was added to the medium or when the puuR gene, which encodes a putative repressor, was deleted. When E. coli was grown in M9-tryptone medium, PuuP was expressed mainly in the exponential growth phase, and PotFGHI was expressed independently of the growth phase.

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