scholarly journals Transcriptional Rewiring, Adaptation, and the Role of Gene Duplication in the Metabolism of Ethanol of Saccharomyces cerevisiae

mSystems ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Beatriz Sabater-Muñoz ◽  
Florian Mattenberger ◽  
Mario A. Fares ◽  
Christina Toft
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Carbon Source ◽  
Gene Duplication ◽  
Growth Parameters ◽  
Small Scale ◽  
Whole Genome ◽  
Duplicated Genes ◽  
Content Type ◽  
Transcriptional Rewiring

ABSTRACT Ethanol is the main by-product of yeast sugar fermentation that affects microbial growth parameters, being considered a dual molecule, a nutrient and a stressor. Previous works demonstrated that the budding yeast arose after an ancient hybridization process resulted in a tier of duplicated genes within its genome, many of them with implications in this ethanol “produce-accumulate-consume” strategy. The evolutionary link between ethanol production, consumption, and tolerance versus ploidy and stability of the hybrids is an ongoing debatable issue. The implication of ancestral duplicates in this metabolic rewiring, and how these duplicates differ transcriptionally, remains unsolved. Here, we study the transcriptomic adaptive signatures to ethanol as a nonfermentative carbon source to sustain clonal yeast growth by experimental evolution, emphasizing the role of duplicated genes in the adaptive process. As expected, ethanol was able to sustain growth but at a lower rate than glucose. Our results demonstrate that in asexual populations a complete transcriptomic rewiring was produced, strikingly by downregulation of duplicated genes, mainly whole-genome duplicates, whereas small-scale duplicates exhibited significant transcriptional divergence between copies. Overall, this study contributes to the understanding of evolution after gene duplication, linking transcriptional divergence with duplicates’ fate in a multigene trait as ethanol tolerance. IMPORTANCE Gene duplication events have been related with increasing biological complexity through the tree of life, but also with illnesses, including cancer. Early evolutionary theories indicated that duplicated genes could explore alternative functions due to relaxation of selective constraints in one of the copies, as the other remains as ancestral-function backup. In unicellular eukaryotes like yeasts, it has been demonstrated that the fate and persistence of duplicates depend on duplication mechanism (whole-genome or small-scale events), shaping their actual genomes. Although it has been shown that small-scale duplicates tend to innovate and whole-genome duplicates specialize in ancestral functions, the implication of duplicates’ transcriptional plasticity and transcriptional divergence on environmental and metabolic responses remains largely obscure. Here, by experimental adaptive evolution, we show that Saccharomyces cerevisiae is able to respond to metabolic stress (ethanol as nonfermentative carbon source) due to the persistence of duplicated genes. These duplicates respond by transcriptional rewiring, depending on their transcriptional background. Our results shed light on the mechanisms that determine the role of duplicates, and on their evolvability.

scholarly journals The Role of Ancestral Duplicated Genes in Adaptation to Growth on Lactate, a Non-Fermentable Carbon Source for the Yeast Saccharomyces cerevisiae

2021 ◽  
Vol 22 (22) ◽  
pp. 12293
Author(s):  
Florian Mattenberger ◽  
Mario A. Fares ◽  
Christina Toft ◽  
Beatriz Sabater-Muñoz
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Carbon Source ◽  
Molecular Mechanisms ◽  
Functional Divergence ◽  
Small Scale ◽  
Whole Genome ◽  
Duplicated Genes ◽  
Acidic Stress ◽  
Yeast Saccharomyces Cerevisiae ◽  
Transcriptomic Response

The cell central metabolism has been shaped throughout evolutionary times when facing challenges from the availability of resources. In the budding yeast, Saccharomyces cerevisiae, a set of duplicated genes originating from an ancestral whole-genome and several coetaneous small-scale duplication events drive energy transfer through glucose metabolism as the main carbon source either by fermentation or respiration. These duplicates (~a third of the genome) have been dated back to approximately 100 MY, allowing for enough evolutionary time to diverge in both sequence and function. Gene duplication has been proposed as a molecular mechanism of biological innovation, maintaining balance between mutational robustness and evolvability of the system. However, some questions concerning the molecular mechanisms behind duplicated genes transcriptional plasticity and functional divergence remain unresolved. In this work we challenged S. cerevisiae to the use of lactic acid/lactate as the sole carbon source and performed a small adaptive laboratory evolution to this non-fermentative carbon source, determining phenotypic and transcriptomic changes. We observed growth adaptation to acidic stress, by reduction of growth rate and increase in biomass production, while the transcriptomic response was mainly driven by repression of the whole-genome duplicates, those implied in glycolysis and overexpression of ROS response. The contribution of several duplicated pairs to this carbon source switch and acidic stress is also discussed.

scholarly journals Whole-genome sequencing from the New Zealand Saccharomyces cerevisiae population reveals the genomic impacts of novel microbial range expansion

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Peter Higgins ◽  
Cooper A Grace ◽  
Soon A Lee ◽  
Matthew R Goddard
Keyword(s):  
Saccharomyces Cerevisiae ◽  
New Zealand ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Range Expansion ◽  
Copy Number ◽  
Small Scale ◽  
Whole Genome ◽  
Copy Number Changes ◽  
The Impact

Abstract Saccharomyces cerevisiae is extensively utilized for commercial fermentation, and is also an important biological model; however, its ecology has only recently begun to be understood. Through the use of whole-genome sequencing, the species has been characterized into a number of distinct subpopulations, defined by geographical ranges and industrial uses. Here, the whole-genome sequences of 104 New Zealand (NZ) S. cerevisiae strains, including 52 novel genomes, are analyzed alongside 450 published sequences derived from various global locations. The impact of S. cerevisiae novel range expansion into NZ was investigated and these analyses reveal the positioning of NZ strains as a subgroup to the predominantly European/wine clade. A number of genomic differences with the European group correlate with range expansion into NZ, including 18 highly enriched single-nucleotide polymorphism (SNPs) and novel Ty1/2 insertions. While it is not possible to categorically determine if any genetic differences are due to stochastic process or the operations of natural selection, we suggest that the observation of NZ-specific copy number increases of four sugar transporter genes in the HXT family may reasonably represent an adaptation in the NZ S. cerevisiae subpopulation, and this correlates with the observations of copy number changes during adaptation in small-scale experimental evolution studies.

Societal discontent will increase in Bahrain

2021 ◽  
Keyword(s):  
Large Scale ◽  
Political Representation ◽  
Social Protest ◽  
Small Scale ◽  
Content Type ◽  
High Profile ◽  
Arab Uprisings ◽  
Base Level

Significance Although large-scale social protest in Bahrain has been cowed over the ten years since the ‘Arab uprisings’, small-scale demonstrations recur, reflecting a base level of discontent. Mobilising issues include economic pressures, limited political representation (especially of the Shia majority) and, most recently, ties with Israel. Impacts Despite protests, Israel’s and Bahrain’s respective ambassadors will keep up high-profile activity and statements. The authorities are likely to exaggerate the role of Iranian interference in order to deepen the Sunni-Shia divide. If Riyadh manages to extricate itself from the Yemen war, that could partly reduce the pressure on Manama.

scholarly journals Determination of the Global Pattern of Gene Expression in Yeast Cells by Intracellular Levels of Guanine Nucleotides

mBio ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Andy Hesketh ◽  
Marta Vergnano ◽  
Stephen G. Oliver
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Carbon Source ◽  
Gene Transcription ◽  
Adenine Nucleotide ◽  
High Energy ◽  
Yeast Cells ◽  
Purine Nucleotides ◽  
Global Pattern ◽  
Content Type

ABSTRACT Correlations between gene transcription and the abundance of high-energy purine nucleotides in Saccharomyces cerevisiae have often been noted. However, there has been no systematic investigation of this phenomenon in the absence of confounding factors such as nutrient status and growth rate, and there is little hard evidence for a causal relationship. Whether transcription is fundamentally responsive to prevailing cellular energetic conditions via sensing of intracellular purine nucleotides, independently of specific nutrition, remains an important question. The controlled nutritional environment of chemostat culture revealed a strong correlation between ATP and GTP abundance and the transcription of genes required for growth. Short pathways for the inducible and futile consumption of ATP or GTP were engineered into S. cerevisiae, permitting analysis of the transcriptional effect of an increased demand for these nucleotides. During steady-state growth using the fermentable carbon source glucose, the futile consumption of ATP led to a decrease in intracellular ATP concentration but an increase in GTP and the guanylate energy charge (GEC). Expression of transcripts encoding proteins involved in ribosome biogenesis, and those controlled by promoters subject to SWI/SNF-dependent chromatin remodelling, was correlated with these nucleotide pool changes. Similar nucleotide abundance changes were observed using a nonfermentable carbon source, but an effect on the growth-associated transcriptional programme was absent. Induction of the GTP-cycling pathway had only marginal effects on nucleotide abundance and gene transcription. The transcriptional response of respiring cells to glucose was dampened in chemostats induced for ATP cycling, but not GTP cycling, and this was primarily associated with altered adenine nucleotide levels. IMPORTANCE This paper investigates whether, independently of the supply of any specific nutrient, gene transcription responds to the energy status of the cell by monitoring ATP and GTP levels. Short pathways for the inducible and futile consumption of ATP or GTP were engineered into the yeast Saccharomyces cerevisiae, and the effect of an increased demand for these purine nucleotides on gene transcription was analyzed. The resulting changes in transcription were most consistently associated with changes in GTP and GEC levels, although the reprogramming in gene expression during glucose repression is sensitive to adenine nucleotide levels. The results show that GTP levels play a central role in determining how genes act to respond to changes in energy supply and that any comprehensive understanding of the control of eukaryotic gene expression requires the elucidation of how changes in guanine nucleotide abundance are sensed and transduced to alter the global pattern of transcription.

scholarly journals The Catabolite Repressor/Activator Cra Is a Bridge Connecting Carbon Metabolism and Host Colonization in the Plant Drought Resistance-Promoting Bacterium Pantoea alhagi LTYR-11Z

2018 ◽  
Vol 84 (13) ◽  
Author(s):  
Lei Zhang ◽  
Muhang Li ◽  
Qiqi Li ◽  
Chaoqiong Chen ◽  
Meng Qu ◽  
...  
Keyword(s):  
Carbon Source ◽  
Carbon Metabolism ◽  
Carbon Sources ◽  
Endophytic Bacterium ◽  
Bacterial Attachment ◽  
Gene Encoding ◽  
Wheat Roots ◽  
Host Colonization ◽  
Content Type

ABSTRACT Efficient root colonization is a prerequisite for application of plant growth-promoting (PGP) bacteria in improving health and yield of agricultural crops. We have recently identified an endophytic bacterium, Pantoea alhagi LTYR-11Z, with multiple PGP properties that effectively colonizes the root system of wheat and improves its growth and drought tolerance. To identify novel regulatory genes required for wheat colonization, we screened an LTYR-11Z transposon (Tn) insertion library and found cra to be a colonization-related gene. By using transcriptome (RNA-seq) analysis, we found that transcriptional levels of an eps operon, the ydiV gene encoding an anti-FlhD 4 C 2 factor, and the yedQ gene encoding an enzyme for synthesis of cyclic dimeric GMP (c-di-GMP) were significantly downregulated in the Δ cra mutant. Further studies demonstrated that Cra directly binds to the promoters of the eps operon, ydiV , and yedQ and activates their expression, thus inhibiting motility and promoting exopolysaccharide (EPS) production and biofilm formation. Consistent with previous findings that Cra plays a role in transcriptional regulation in response to carbon source availability, the activating effects of Cra were much more pronounced when LTYR-11Z was grown within a gluconeogenic environment than when it was grown within a glycolytic environment. We further demonstrate that the ability of LTYR-11Z to colonize wheat roots is modulated by the availability of carbon sources. Altogether, these results uncover a novel strategy utilized by LTYR-11Z to achieve host colonization in response to carbon nutrition in the environment, in which Cra bridges a connection between carbon metabolism and colonization capacity of LTYR-11Z. IMPORTANCE Rapid and appropriate response to environmental signals is crucial for bacteria to adapt to competitive environments and to establish interactions with their hosts. Efficient colonization and persistence within the host are controlled by various regulatory factors that respond to specific environmental cues. The most common is nutrient availability. In this work, we unraveled the pivotal role of Cra in regulation of colonization ability of Pantoea alhagi LTYR-11Z in response to carbon source availability. Moreover, we identified three novel members of the Cra regulon involved in EPS synthesis, regulation of flagellar biosynthesis, and synthesis of c-di-GMP and propose a working model to explain the Cra-mediated regulatory mechanism that links carbon metabolism to host colonization. This study elucidates the regulatory role of Cra in bacterial attachment and colonization of plants, which raises the possibility of extending our studies to other bacteria associated with plant and human health.

scholarly journals Exploring the role of volunteers in social care for older adults

2020 ◽  
Vol 21 (2) ◽  
pp. 129-139 ◽  
Author(s):  
Ailsa Cameron ◽  
Eleanor K. Johnson ◽  
Paul B. Willis ◽  
Liz Lloyd ◽  
Randall Smith
Keyword(s):  
Older Adults ◽  
Older People ◽  
Social Care ◽  
Evidence Base ◽  
Care Staff ◽  
Small Scale ◽  
The South ◽  
Content Type ◽  
South West

Purpose This paper aims to report the findings of a study that explores the contribution volunteers make to social care for older adults, identifying lessons for the social care sector and policymakers. Design/methodology/approach An exploratory multiple case study design was used to capture the perspectives and experiences of managers of services, volunteer co-ordinators, volunteers, paid care staff and older people. Seven diverse social care organisations took part in the study drawn from three locations in the South West of England. Findings This study identified three distinct models of volunteer contribution to social care services for older people. Although the contributions made by volunteers to services are valued, the study drew attention to some of the challenges related to their involvement. Research limitations/implications The organisations taking part in this small-scale study were all based in the South West of England, and the findings are therefore not generalisable but contribute to the growing evidence base related to this important field. Practical implications This study demonstrates the importance of the volunteer co-ordinator role and suggests that it is properly funded and resourced. It also confirms the importance of volunteers receiving appropriate training and support. Originality/value Given the increasing involvement of volunteers in the provision of social care, this paper provides lessons to ensure the role of volunteers in social care enhances rather than diminishes the quality of care provided.

Entrepreneurial orientation and the mediating role of organisational learning amongst Indian S-SMEs

2019 ◽  
Vol 26 (5) ◽  
pp. 641-660 ◽  
Author(s):  
Stanzin Mantok ◽  
Harjit Sekhon ◽  
Gurjeet Kaur Sahi ◽  
Paul Jones
Keyword(s):  
Entrepreneurial Orientation ◽  
Business Performance ◽  
Organisational Learning ◽  
Systematic Sampling ◽  
Small Scale ◽  
Content Type ◽  
Mediating Role ◽  
Strategic Orientations ◽  
Competitor Orientation

Purpose The purpose of this paper is to examine organisational learning as a mediator among small-scale manufacturing enterprises (S-SMEs) which comprise the majority of economic activity in an emergent/developing economy. This study offers further understanding regarding the mediating role of organisational learning in developing world economies, due to its potential regional influence. Design/methodology/approach A cross-sectional survey of Indian S-SMEs was undertaken from the District Industrial Center. The study employed a systematic sampling technique to contact owner/managers. Overall, 204 S-SMEs owners/managers participated in the study and 192 usable survey instruments were received. Findings The study offers novel insights to the following questions. First, the factors that prompt entrepreneurial orientation to achieve superior business performance, i.e. the antecedents of entrepreneurial orientation? The results reveal competitor orientation is an antecedent of entrepreneurial orientation that leads to an S-SME’s business performance. Second, the outcomes of entrepreneurial orientation, i.e. the consequences of entrepreneurial orientation? The study reveals organisational learning and business performance are the corollary of entrepreneurial orientation. Third, the examination of whether organisational learning mediates the relationship between entrepreneurial orientation and business performance? The findings found the effects of entrepreneurial orientation on business performance are, in part, mediated by organisational learning. Research limitations/implications Three study limitations are recognised. First, other strategic orientations, including technology orientation, production orientation and selling orientation are not included. Second, other constructs have a potentially significant relationship with market and entrepreneurial orientation, such as organisational capabilities, innovation and social context, were not considered. Third, the study is industry-sector specific and does not consider alternative sectors which also may play a potential role in economic development. Originality/value This study enhances the existing S-SME literature by identifying factors contributing to entrepreneurial orientation and its repercussions on business performance. For S-SMEs it adds credence to the role played by organisational learning in mediating the link between entrepreneurial orientation and business performance which potentially encourages owner/managers to dedicate increased time and resources towards creating and maintaining a conducive learning environment. The results support entrepreneurs in acknowledging the importance of competitor orientation during the emergence and development of entrepreneurial orientation, specifically in emerging economy contexts.

scholarly journals Engineered Pentafunctional Minicellulosome for Simultaneous Saccharification and Ethanol Fermentation in Saccharomyces cerevisiae

2014 ◽  
Vol 80 (21) ◽  
pp. 6677-6684 ◽  
Author(s):  
Youyun Liang ◽  
Tong Si ◽  
Ee Lui Ang ◽  
Huimin Zhao
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Carbon Source ◽  
Phosphoric Acid ◽  
Sole Carbon Source ◽  
Consolidated Bioprocessing ◽  
Content Type ◽  
Yeast Strains ◽  
Recombinant Yeast Strain ◽  
Polysaccharide Monooxygenases ◽  
Simultaneous Saccharification

ABSTRACTSeveral yeast strains have been engineered to express different cellulases to achieve simultaneous saccharification and fermentation of lignocellulosic materials. However, successes in these endeavors were modest, as demonstrated by the relatively low ethanol titers and the limited ability of the engineered yeast strains to grow using cellulosic materials as the sole carbon source. Recently, substantial enhancements to the breakdown of cellulosic substrates have been observed when lytic polysaccharide monooxygenases (LPMOs) were added to traditional cellulase cocktails. LPMOs are reported to cleave cellulose oxidatively in the presence of enzymatic electron donors such as cellobiose dehydrogenases. In this study, we coexpressed LPMOs and cellobiose dehydrogenases with cellobiohydrolases, endoglucanases, and β-glucosidases inSaccharomyces cerevisiae. These enzymes were secreted and docked onto surface-displayed miniscaffoldins through cohesin-dockerin interaction to generate pentafunctional minicellulosomes. The enzymes on the miniscaffoldins acted synergistically to boost the degradation of phosphoric acid swollen cellulose and increased the ethanol titers from our previously achieved levels of 1.8 to 2.7 g/liter. In addition, the newly developed recombinant yeast strain was also able to grow using phosphoric acid swollen cellulose as the sole carbon source. The results demonstrate the promise of the pentafunctional minicellulosomes for consolidated bioprocessing by yeast.

scholarly journals The Roles of Whole-Genome and Small-Scale Duplications in the Functional Specialization of Saccharomyces cerevisiae Genes

PLoS Genetics ◽  
2013 ◽  
Vol 9 (1) ◽  
pp. e1003176 ◽  
Author(s):  
Mario A. Fares ◽  
Orla M. Keane ◽  
Christina Toft ◽  
Lorenzo Carretero-Paulet ◽  
Gary W. Jones
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Small Scale ◽  
Functional Specialization ◽  
Whole Genome

scholarly journals Interplay of a Ligand Sensor and an Enzyme in Controlling Expression of the Saccharomyces cerevisiae GAL Genes

2011 ◽  
Vol 11 (3) ◽  
pp. 334-342 ◽  
Author(s):  
Dariusz Abramczyk ◽  
Stacey Holden ◽  
Christopher J. Page ◽  
Richard J. Reece
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Transcriptional Control ◽  
Transcriptional Response ◽  
Content Type ◽  
Considerable Debate ◽  
Active Transcription ◽  
Gal Genes ◽  
The Subject

ABSTRACT The regulation of the Saccharomyces cerevisiae GAL genes in response to galactose as a source of carbon has served as a paradigm for eukaryotic transcriptional control over the last 50 years. Three proteins—a transcriptional activator (Gal4p), an inhibitor (Gal80p), and a ligand sensor (Gal3p)—control the switch between inert and active gene expression. The molecular mechanism by which the recognition of galactose within the cell is converted into a transcriptional response has been the subject of considerable debate. In this study, using a novel and powerful method of localizing active transcription factors within the nuclei of cells, we show that a short-lived complex between Gal4p, Gal80p, and Gal3p occurs soon after the addition of galactose to cells to activate GAL gene expression. Gal3p is subsequently replaced in this complex by Gal1p, and a Gal4p-Gal80p-Gal1p complex is responsible for the continued expression of the GAL genes. The transient role of the ligand sensor indicates that current models for the induction and continued expression of the yeast GAL genes need to be reevaluated.

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