scholarly journals Polymorphisms in the yeast galactose sensor underlie a natural continuum of nutrient-decision phenotypes

2017 ◽  
Author(s):  
Kayla B. Lee ◽  
Jue Wang ◽  
Julius Palme ◽  
Renan Escalante-Chong ◽  
Bo Hua ◽  
...  
Keyword(s):  
Allelic Variation ◽  
Natural Environments ◽  
Ecological Constraints ◽  
Single Protein ◽  
Natural Isolates ◽  
Gal Genes ◽  
Diauxic Lag ◽  
Different Strains ◽  
Nutrient Changes ◽  
Time Required

AbstractIn nature, microbes often need to “decide” which of several available nutrients to utilize, a choice that depends on a cell’s inherent preference and external nutrient levels. While natural environments can have mixtures of different nutrients, phenotypic variation in microbes’ decisions of which nutrient to utilize is poorly studied. Here, we quantified differences in the concentration of glucose and galactose required to induce galactose-responsive (GAL) genes across 36 wildS. cerevisiaestrains. Using bulk segregant analysis, we found that a locus containing the galactose sensorGAL3was associated with differences in GAL signaling in eight different crosses. Using allele replacements, we confirmed thatGAL3is the major driver of GAL induction variation, and thatGAL3allelic variation alone can explain as much as 90% of the variation in GAL induction in a cross. TheGAL3variants we found modulate the diauxic lag, a selectable trait. These results suggest that ecological constraints on the galactose pathway may have led to variation in a single protein, allowing cells to quantitatively tune their response to nutrient changes in the environment.Author summaryIn nature, microbes often need to decide which of many potential nutrients to consume. This decision making process is complex, involving both intracellular constraints and the organism’s perception of the environment. To begin to mimic the complexity of natural environments, we grew cells in mixtures of two sugars, glucose and galactose. We find that in mixed environments, the sugar concentration at which cells decides to induce galactose-utilizing (GAL) genes is highly variable in natural isolates of yeast. By analyzing crosses of phenotypically different strains, we identified a locus containing the galactose sensor, a gene that in theory could allow cells to tune their perception of the environment. We confirmed that the galactose sensor can explain upwards of 90% of the variation in the decision to induce GAL genes. Finally, we show that the variation in the galactose sensor can modulate the time required for cells to switch from utilizing glucose to galactose. Our results suggest that signaling pathways can be highly variable across strains and thereby might allow for rapid adaption in fluctuating environments.

Novel Loci Control Variation in Reproductive Timing inArabidopsis thalianain Natural Environments

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1875-1884 ◽  
Author(s):  
Cynthia Weinig ◽  
Mark C Ungerer ◽  
Lisa A Dorn ◽  
Nolan C Kane ◽  
Yuko Toyonaga ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Allelic Variation ◽  
Developmental Pathways ◽  
Natural Environments ◽  
Reproductive Timing ◽  
Controlled Environments ◽  
Photoperiod Pathway ◽  
Differential Involvement ◽  
Short Days ◽  
Transition To Flowering

AbstractMolecular biologists are rapidly characterizing the genetic basis of flowering in model species such as Arabidopsis thaliana. However, it is not clear how the developmental pathways identified in controlled environments contribute to variation in reproductive timing in natural ecological settings. Here we report the first study of quantitative trait loci (QTL) for date of bolting (the transition from vegetative to reproductive growth) in A. thaliana in natural seasonal field environments and compare the results with those obtained under typical growth-chamber conditions. Two QTL specific to long days in the chamber were expressed only in spring-germinating cohorts in the field, and two loci specific to short days in the chamber were expressed only in fall-germinating cohorts, suggesting differential involvement of the photoperiod pathway in different seasonal environments. However, several other photoperiod-specific QTL with large effects in controlled conditions were undetectable in natural environments, indicating that expression of allelic variation at these loci was overridden by environmental factors specific to the field. Moreover, a substantial number of QTL with major effects on bolting date in one or more field environments were undetectable under controlled environment conditions. These novel loci suggest the involvement of additional genes in the transition to flowering under ecologically relevant conditions.

Neural responses to simple simulated echoes in the auditory brain stem of the unanesthetized rabbit

1995 ◽  
Vol 74 (6) ◽  
pp. 2469-2486 ◽  
Author(s):  
D. C. Fitzpatrick ◽  
S. Kuwada ◽  
R. Batra ◽  
C. Trahiotis
Keyword(s):  
Time Course ◽  
Superior Olivary Complex ◽  
Precedence Effect ◽  
Natural Environments ◽  
Complete Suppression ◽  
Sound Waves ◽  
Neural Basis ◽  
Unanesthetized Rabbit ◽  
Echo Threshold ◽  
Time Required

1. In most natural environments, sound waves from a single source will reach a listener through both direct and reflected paths. Sound traveling the direct path arrives first, and determines the perceived location of the source despite the presence of reflections from many different locations. This phenomenon is called the "law of the first wavefront" or "precedence effect." The time at which the reflection is first perceived as a separately localizable sound defines the end of the precedence window and is called "echo threshold." The precedence effect represents an important property of the auditory system, the neural basis for which has only recently begun to be examined. Here we report the responses of single neurons in the inferior colliculus (IC) and superior olivary complex (SOC) of the unanesthetized rabbit to a sound and its simulated reflection. 2. Stimuli were pairs of monaural or binaural clicks delivered through earphones. The leading click, or conditioner, simulated a direct sound, and the lagging click, or probe, simulated a reflection. Interaural time differences (ITDs) were introduced in the binaural conditioners and probes to adjust their simulated locations. The probe was always set at the neuron's best ITD, whereas the conditioner was set at the neuron's best ITD or its worst ITD. To measure the time course of the effects of the conditioner on the probe, we examined the response to the probe as a function of the conditioner-probe interval (CPI). 3. When IC neurons were tested with conditioners and probes set at the neuron's best ITD, the response to the probe as a function of CPI had one of two forms: early-low or early-high. In early-low neurons the response to the probe was initially suppressed but recovered monotonically at longer CPIs. Early-high neurons showed a nonmonotonic recovery pattern. In these neurons the maximal suppression did not occur at the shortest CPIs, but rather after a period of less suppression. Beyond this point, recovery was similar to that of early-low neurons. The presence of early-high neurons meant that the overall population was never entirely suppressed, even at short CPIs. Taken as a whole. CPIs for 50% recovery of the response to the probe among neurons ranged from 1 to 64 ms with a median of approximately 6 ms. 4. The above results are consistent with the time course of the precedence effect for the following reasons. 1) The lack of complete suppression at any CPI is compatible with behavioral results that show the presence of a probe can be detected even at short CPIs when it is not separately localizable. 2) At a CPI corresponding to echo threshold for human listeners (approximately 4 ms CPI) there was a considerable response to the probe, consistent with it being heard as a separately localizable sound at this CPI. 3) Full recovery for all neurons required a period much longer than that associated with the precedence effect. This is consistent with the relatively long time required for conditioners and probes to be heard with equal loudness. 5. Conditioners with either the best ITD or worst ITD were used to determine the effect of ITD on the response to the probe. The relative amounts of suppression caused by the two ITDs varied among neurons. Some neurons were suppressed about equally by both types of conditioners, others were suppressed more by a conditioner with the best ITD, and still others by a conditioner with the worst ITD. Because the best ITD and worst ITD presumably activate different pathways, these results suggest that different neurons receive a different balance of inhibition from different sources. 6. The recovery functions of neurons not sensitive to ITDs were similar to those of ITD-sensitive, neurons. This suggests that the time course of suppression may be common among different IC populations. 7. We also studied neurons in the SOC. Although many showed binaural interactions, none were sensitive to ITDs. Thus the response of this population may not be

scholarly journals Galactose metabolic genes in yeast respond to a ratio of galactose and glucose

2015 ◽  
Vol 112 (5) ◽  
pp. 1636-1641 ◽  
Author(s):  
Renan Escalante-Chong ◽  
Yonatan Savir ◽  
Sean M. Carroll ◽  
John B. Ingraham ◽  
Jue Wang ◽  
...  
Keyword(s):  
Classical Model ◽  
Nutrient Sensing ◽  
Natural Environments ◽  
Glucose Signaling ◽  
Glucose Levels ◽  
Metabolic Genes ◽  
Wide Range ◽  
Controlled Environments ◽  
Single Input ◽  
Gal Genes

Natural environments are filled with multiple, often competing, signals. In contrast, biological systems are often studied in “well-controlled” environments where only a single input is varied, potentially missing important interactions between signals. Catabolite repression of galactose by glucose is one of the best-studied eukaryotic signal integration systems. In this system, it is believed that galactose metabolic (GAL) genes are induced only when glucose levels drop below a threshold. In contrast, we show that GAL gene induction occurs at a constant external galactose:glucose ratio across a wide range of sugar concentrations. We systematically perturbed the components of the canonical galactose/glucose signaling pathways and found that these components do not account for ratio sensing. Instead we provide evidence that ratio sensing occurs upstream of the canonical signaling pathway and results from the competitive binding of the two sugars to hexose transporters. We show that a mutant that behaves as the classical model expects (i.e., cannot use galactose above a glucose threshold) has a fitness disadvantage compared with wild type. A number of common biological signaling motifs can give rise to ratio sensing, typically through negative interactions between opposing signaling molecules. We therefore suspect that this previously unidentified nutrient sensing paradigm may be common and overlooked in biology.

scholarly journals Analysis of Germination Capacity and Germinant Receptor (Sub)clusters of Genome-Sequenced Bacillus cereus Environmental Isolates and Model Strains

2016 ◽  
Vol 83 (4) ◽  
Author(s):  
Alicja K. Warda ◽  
Yinghua Xiao ◽  
Jos Boekhorst ◽  
Marjon H. J. Wells-Bennik ◽  
Masja N. Nierop Groot ◽  
...  
Keyword(s):  
Bacillus Cereus ◽  
Spore Germination ◽  
Brain Heart Infusion ◽  
Whole Genome Sequence ◽  
Single Spore ◽  
Content Type ◽  
Germination Response ◽  
Natural Isolates ◽  
Heat Activation ◽  
Different Strains

ABSTRACT Spore germination of 17 Bacillus cereus food isolates and reference strains was evaluated using flow cytometry analysis in combination with fluorescent staining at a single-spore level. This approach allowed for rapid collection of germination data under more than 20 conditions, including heat activation of spores, germination in complex media (brain heart infusion [BHI] and tryptone soy broth [TSB]), and exposure to saturating concentrations of single amino acids and the combination of alanine and inosine. Whole-genome sequence comparison revealed a total of 11 clusters of operons encoding germinant receptors (GRs): GerK, GerI, and GerL were present in all strains, whereas GerR, GerS, GerG, GerQ, GerX, GerF, GerW, and GerZ (sub)clusters showed a more diverse presence/absence in different strains. The spores of tested strains displayed high diversity with regard to their sensitivity and responsiveness to selected germinants and heat activation. The two laboratory strains, B. cereus ATCC 14579 and ATCC 10987, and 11 food isolates showed a good germination response under a range of conditions, whereas four other strains (B. cereus B4085, B4086, B4116, and B4153) belonging to phylogenetic group IIIA showed a very weak germination response even in BHI and TSB media. Germination responses could not be linked to specific (combinations of) GRs, but it was noted that the four group IIIA strains contained pseudogenes or variants of subunit C in their gerL cluster. Additionally, two of those strains (B4086 and B4153) carried pseudogenes in the gerK and gerR I (sub)clusters that possibly affected the functionality of these GRs. IMPORTANCE Germination of bacterial spores is a critical step before vegetative growth can resume. Food products may contain nutrient germinants that trigger germination and outgrowth of Bacillus species spores, possibly leading to food spoilage or foodborne illness. Prediction of spore germination behavior is, however, very challenging, especially for spores of natural isolates that tend to show more diverse germination responses than laboratory strains. The approach used has provided information on the genetic diversity in GRs and corresponding subclusters encoded by B. cereus strains, as well as their germination behavior and possible associations with GRs, and it provides a basis for further extension of knowledge on the role of GRs in B. cereus (group member) ecology and transmission to the host.

scholarly journals Caenorhabditis elegans nematodes are not attracted to the terrestrial isopod Porcellio scaber

2020 ◽  
Author(s):  
Heather Archer ◽  
Selina Deiparine ◽  
Erik C. Andersen
Keyword(s):  
Caenorhabditis Elegans ◽  
Wild Strain ◽  
Adult Life ◽  
The Body ◽  
Natural Environments ◽  
Porcellio Scaber ◽  
Wild Isolate ◽  
Terrestrial Isopods ◽  
C Elegans ◽  
Different Strains

ABSTRACTPhoresy is a behavior in which an organism, the phoront, travels from one location to another by ‘hitching a ride’ on the body of a host as it disperses. Some phoronts are generalists, taking advantage of any available host. Others are specialists and travel only when specific hosts are located using chemical cues to identify and move (chemotax) toward the preferred host. Free-living nematodes, like Caenorhabditis elegans, are often found in natural environments that contain terrestrial isopods and other invertebrates. Additionally, the C. elegans wild strain PB306 was isolated associated with the isopod Porcellio scaber. However, it is currently unclear if C. elegans is a phoront of terrestrial isopods, and if so, whether it is a specialist, generalist, or developmental stage-specific combination of both strategies. Because the relevant chemical stimuli might be secreted compounds or volatile odorants, we used different types of chemotaxis assays across diverse extractions of compounds or odorants to test whether C. elegans is attracted to P. scaber. We show that two different strains – the wild isolate PB306 and the laboratory-adapted strain N2 – are not attracted to P. scaber during either the dauer or adult life stages. Our results indicate that C. elegans was not attracted to chemical compounds or volatile odorants from P. scaber, providing valuable empirical evidence to suggest that any associations between these two species are likely opportunistic rather than specific phoresy.

scholarly journals Campylobacter jejunitranscriptome changes during loss of culturability in water

2017 ◽  
Author(s):  
Christina Bronowski ◽  
Kasem Mustafa ◽  
Ian B. Goodhead ◽  
Chloe E. James ◽  
Charlotte Nelson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Sampling Time ◽  
Natural Environments ◽  
Rapid Loss ◽  
Potential Reservoir ◽  
Different Temperatures ◽  
Bacterial Gastroenteritis ◽  
Flagellar Assembly ◽  
Different Strains ◽  
Considerable Loss

AbstractBackgroundThe natural environment serves as a potential reservoir forCampylobacter,the leading cause of bacterial gastroenteritis in humans. However, little is understood about the mechanisms underlying variations in survival characteristics between different strains ofC. jejuniin natural environments, including water.ResultsWe identified threeCampylobacter jejunistrains that exhibited variability in their ability to retain culturability after suspension in water at two different temperatures (4°C and 25°C). Of the three, strainsC. jejuniM1 exhibited the most rapid loss of culturability whilst retaining viability. Using RNAseq transcriptomics, we characterised C.jejuniM1 gene expression in response to suspension in water by analyzing bacterial suspensions recovered immediately after introduction into water (Time 0), and from two sampling time/temperature combinations where considerable loss of culturability was evident, namely (i) after 24 h at 25°C, and (ii) after 72 h at 4°C. Transcript data were compared with a culture-grown control. Some gene expression characteristics were shared amongst the three populations recovered from water, with more genes being up-regulated than down. Many of the up-regulated genes were identified in the Time 0 sample, whereas the majority of down-regulated genes occurred in the 25°C (24 h) sample.ConclusionsVariations in expression were found amongst genes associated with oxygen tolerance, starvation and osmotic stress. However, we also found upregulation of flagellar assembly genes, accompanied by down-regulation of genes involved in chemotaxis. Our data also suggested a switch from secretion via thesecsystem to via thetatsystem, and that the quorum sensing geneluxSmay be implicated in the survival of strain M1 in water. Variations in gene expression also occurred in accessory genome regions. Our data suggest that despite the loss of culturability,C. jejuniM1 remains viable and adapts via specific changes in gene expression.

scholarly journals Fluctuating environment can negate cheater success due to speed-agility trade-off

2021 ◽  
Author(s):  
Naomi Iris van den Berg ◽  
Lajos Kalmar ◽  
Kiran Raosaheb Patil
Keyword(s):  
Evolutionary Dynamics ◽  
Temporal Dynamics ◽  
Plant Root ◽  
Evolutionary Game ◽  
Spatial Segregation ◽  
Growth Speed ◽  
Trade Off ◽  
Natural Systems ◽  
Diauxic Lag ◽  
Time Required

Stability of microbial cooperation through common goods is susceptible to cheating. Evidence suggests that cheating plays a less prominent role in many natural systems than hitherto predicted by models of eco-evolutionary dynamics and evolutionary game theory. While several cheater negating factors such as spatial segregation have been identified, most consider single-nutrient regimes. Here we propose a cheater-suppressing mechanism based on previous experimental observations regarding the biochemical trade-off between growth speed and delay in switching to alternative nutrients. As changing the nutrient source requires redistribution of enzymatic resources to different metabolic pathways, the advantage in speed is offset by lower agility due to longer time required for resource re-allocation. Using an in silico model system of sucrose utilisation by Saccharomyces cerevisiae, we find that a trade-off between growth rate and diauxic lag duration can supress cheaters under fluctuating nutrient availability and thereby stabilise cooperation. The resulting temporal dynamics constrain cheaters despite their competitive benefit for the growth on the primary nutrient via avoided public goods synthesis costs. We further show that this speed-agility trade-off can function in synergy with spatial segregation to avoid the collapse of the community due to the cheaters. Taken together, the growth-agility trade-off may contribute to cheater suppression in microbial ecosystems experiencing fluctuating environments, such as plant root microbiota and gut microbiota.

scholarly journals Plasmid pattern analysis of natural bacterial isolates and its epidemiological implication

1983 ◽  
Vol 90 (3) ◽  
pp. 475-488 ◽  
Author(s):  
E. Tietze ◽  
H. Tschäpe
Keyword(s):  
Pattern Analysis ◽  
Phage Type ◽  
Laboratory Method ◽  
Epidemic Strain ◽  
Bacterial Strains ◽  
E Coli ◽  
Long Time ◽  
Natural Isolates ◽  
Providencia Stuartii ◽  
Different Strains

SUMMARYNatural isolates ofEscherichia coli, Salmonella typhimurium, Klebsiella pneumoniae, andProvidencia stuartiiwere analysed to determine their plasmid content. This data allowed the identification of nosocomial strains ofK. pneumoniaeandP. stuartiiand helped in the differentiation of epidemic strains ofE. coli0111 andS. typhimurium. Phenotypically similar isolates ofS. typhimuriumcould be shown to be of independent origin using plasmid pattern analysis. The dissemination of a particular plasmid through different strains ofS. typhimuriumresulted in a simulation of a very widely distributed epidemic strain, because the plasmid interfered with the phage type of its host strain in addition to determining re sistance properties. Plasmid pattern analysis disclosed two independently existing but interacting epidemic processes: a bacterial ‘epidemic’ strain may become disseminated over a large territory and may predominate there for a long time; a single plasmid, however, may also become distributed through many different bacterial strains and may spread over a large territory. Plasmid pattern analysis provides a valuable and universal epidemiological laboratory method.

scholarly journals Studies on the assembly and secretion of a multicomponent protein. The biosynthesis of vitellogenin, an oestrogen-induced glycolipophosphoprotein

1973 ◽  
Vol 132 (3) ◽  
pp. 459-463 ◽  
Author(s):  
A. H. Merry ◽  
P. J. Dolphin ◽  
K. A. Munday ◽  
M. Akhtar
Keyword(s):  
Polypeptide Chain ◽  
Lag Phase ◽  
Pulse Labelling ◽  
Tissue Protein ◽  
Liver Slices ◽  
Single Protein ◽  
Time Required ◽  
Total Tissue ◽  
Cumulative Evidence

1. Incorporation of [32P]Pi and [3H]leucine into vitellogenin secreted in vitro by liver slices from oestrogen-treated Xenopus laevis is accompanied by a 2h lag; no lag is apparent for the incorporation into total tissue protein. 2. The addition of cycloheximide was found immediately to inhibit further incorporation of radioactive leucine into total tissue protein. The incorporation into secreted vitellogenin, however, continued for 2h after the addition of cycloheximide. 3. Pulse-labelling of liver slices with [3H]leucine for 30min, followed by a chase with a large excess of unlabelled leucine, resulted in the appearance of radioactivity in secreted vitellogenin from 90min after the end of the pulse period. 4. Evidence is presented which suggests that of the radioactivity from [3H]leucine incorporated into proteins by the liver of oestrogen-treated Xenopus some 70% is present in the single protein vitellogenin. 5. The incorporation of [32P]Pi into vitellogenin followed a pattern identical with that found for [3H]leucine in the pulse-labelling experiments and this indicates that synthesis of the polypeptide chain and incorporation of Pi are closely linked processes. 6. The cumulative evidence suggests that the 2h lag phase represents the time required for the assembly and secretion of this multicomponent protein.

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