The yeast Saccharomyces cerevisiae has been an essential component of human civilization because of its long global history of use in food and beverage fermentation. However, the diversity and ...evolutionary history of the domesticated populations of the yeast remain elusive. We show here that China/Far East Asia is likely the center of origin of the domesticated populations of the species. The domesticated populations form two major groups associated with solid- and liquid-state fermentation and appear to have originated from heterozygous ancestors, which were likely formed by outcrossing between diverse wild isolates primitively for adaptation to maltose-rich niches. We found consistent gene expansion and contraction in the whole domesticated population, as well as lineage-specific genome variations leading to adaptation to different environments. We show a nearly panoramic view of the diversity and life history of S. cerevisiae and provide new insights into the origin and evolution of the species.
The wild yeast Saccharomyces paradoxus has become a new model in ecology and evolutionary biology. Different lineages of S. paradoxus have been recognized across the world, but the distribution and ...genetic diversity of the species remain unknown in China, where the origin of its sibling species S. cerevisiae lies. In this study, we investigated the ecological and geographic distribution of S. paradoxus through an extensive field survey in China and performed population genomic analysis on a set of S. paradoxus strains, including 27 strains, representing different geographic and ecological origins within China, and 59 strains representing all the known lineages of the species recognized in the other regions of the world so far. We found two distinct lineages of S. paradoxus in China. The majority of the Chinese strains studied belong to the Far East lineage, and six strains belong to a novel highly diverged lineage. The distribution of these two lineages overlaps ecologically and geographically in temperate to subtropical climate zones in China. With the addition of the new China lineage, the Eurasian population of S. paradoxus exhibits higher genetic diversity than the American population. We observed more possible lineage‐specific introgression events from the Eurasian lineages than from the American lineages. Our results expand the knowledge on ecology, genetic diversity, biogeography, and evolution of S. paradoxus.
Take away
S. paradoxus is distributed in temperate to subtropical climate zones in China.
A novel highly diverged ancient lineage of S. paradoxus is identified.
S. paradoxus exhibits higher genetic diversity in Eurasia than in America.
Saccharomyces paradoxus is distributed in temperate to subtropical climate zones in China. Chinese S. paradoxus strains cluster with the Far East lineage and a novel highly diverged lineage. The Eurasian population of S. paradoxus exhibits higher genetic diversity and more possible HGT/introgression events than the American population.
Chronic airway inflammation mediated by CD8+T lymphocytes contributes to the pathogenesis of Chronic obstructive pulmonary disease (COPD). Deciphering the fingerprint of the chronic inflammation ...orchestrated by CD8+T cells may allow the development of novel approaches to COPD management. Here, the expression of IL‐27 and IFN‐γ+CD8+Tc1 cells were evaluated in patients with COPD and in cigarette smoke‐exposed mice. The production of IL‐27 by marrow‐derived dendritic cells (mDCs) in response to cigarette smoke extract (CSE) was assessed. The role of IL‐27 in IFN‐γ+CD8+Tc1 cells was explored. We demonstrated that elevated IL‐27 was accompanied by an exaggerated IFN‐γ+CD8+Tc1 response in a smoking mouse model of emphysema. We noted that lung dendritic cells were one of the main sources of IL‐27 during chronic cigarette smoke exposure. Moreover, CSE directly induced the production of IL‐27 by mDCs in vitro. IL‐27 negatively regulated the differentiation of IFN‐γ+CD8+Tc1 cells isolated from cigarette smoke‐exposed mice in a STAT1‐ and STAT3‐independent manner. Systemic administration of recombinant IL‐27 attenuated IFN‐γ+CD8+Tc1 response in the late phase of cigarette smoke exposure. Our results uncovered that IL‐27 negatively regulates IFN‐γ+CD8+Tc1 response in the late stage of chronic cigarette smoke exposure, which may provide a new strategy for the anti‐inflammatory treatment of smoking‐related COPD/emphysema.
Cigarette smoke serves as an exogenous dangerous factor promoting the secretion of IL‐27 by mDCs in vitro. In an experimental emphysema mouse model, IL‐27 negatively regulates IFN‐γ+CD8+Tc1 response in the late stage of chronic cigarette smoke exposure via a p‐STAT1 or p‐STAT3 independent manner.
Glucose repression is a central regulatory system in yeast that ensures the utilization of carbon sources in a highly economical manner. The galactose (GAL) metabolism network is stringently ...regulated by glucose repression in yeast and has been a classic system for studying gene regulation. We show here that a Saccharomyces cerevisiae (S. cerevisiae) lineage in spontaneously fermented milk has swapped all its structural GAL genes (GAL2 and the GAL7-10-1 cluster) with early diverged versions through introgression. The rewired GAL network has abolished glucose repression and conversed from a strictly inducible to a constitutive system through polygenic changes in the regulatory components of the network, including a thymine (T) to cytosine (C) and a guanine (G) to adenine (A) transition in the upstream repressing sequence (URS) sites of GAL1 and GAL4, respectively, which impair Mig1p-mediated repression, loss of function of the repressor Gal80p through a T146I substitution in the protein, and subsequent futility of GAL3. Furthermore, the milk lineage of S. cerevisiae has achieved galactose-utilization rate elevation and galactose-over-glucose preference switch through the duplication of the introgressed GAL2 and the loss of function of the main glucose transporter genes HXT6 and HXT7. In addition, we demonstrate that GAL2 requires GAL7 or GAL10 for its expression, and Gal2p likely requires Gal1p for its transportation function in the milk lineage of S. cerevisiae. We show a clear case of reverse evolution of a classic gene network for ecological adaptation and provide new insights into the regulatory model of the canonical GAL network.
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•A milk-adapted yeast lineage harbors early diverged versions of the structural GAL genes•The rewired GAL network is constitutively expressed and abolishes glucose repression•The adapted lineage prefers galactose to glucose, but it can co-utilize both sugars•GAL2 requires GAL7 or GAL10 for its expression and GAL1 for its function
Duan et al. show that a milk-adapted yeast lineage harbors early diverged versions of the structural GAL genes. The rewired GAL network expresses constitutively and abolishes glucose repression. The adapted lineage prefers galactose to glucose, but it can co-utilize both sugars. GAL2 requires GAL7 or GAL10 for its expression and GAL1 for its function.
Recent studies on population genomics of
have substantially improved our understanding of the genetic diversity and domestication history of the yeast. However, the origin of the domesticated ...population of
and the genomic changes responsible for ecological adaption of different populations and lineages remain to be fully revealed. Here we sequenced 64 African strains from various indigenous fermented foods and forests in different African countries and performed a population genomic analysis on them combined with a set of previously sequenced worldwide
strains representing the maximum genetic diversity of the species documented so far. The result supports the previous observations that the wild and domesticated populations of
are clearly separated and that the domesticated population diverges into two distinct groups associated with solid- and liquid-state fermentations from a single ancestor. African strains are mostly located in basal lineages of the two domesticated groups, implying a long domestication history of yeast in Africa. We identified genes that mainly or exclusively occur in specific groups or lineages and genes that exhibit evident group or lineage specific allele distribution patterns. Notably, we show that the homing endonuclease VDE is generally absent in the wild but commonly present in the domesticated lineages of
. The genes with group specific allele distribution patterns are mostly enriched in functionally similar or related fundamental metabolism processes, including the evolutionary conserved TOR signaling pathway.
The baker's yeast
has become a powerful model in ecology and evolutionary biology. A global effort on field survey and population genetics and genomics of
in past decades has shown that the yeast ...distributes ubiquitously in nature with clearly structured populations. The global genetic diversity of
is mainly contributed by strains from Far East Asia, and the ancient basal lineages of the species have been found only in China, supporting an 'out-of-China' origin hypothesis. The wild and domesticated populations are clearly separated in phylogeny and exhibit hallmark differences in sexuality, heterozygosity, gene copy number variation (CNV), horizontal gene transfer (HGT) and introgression events, and maltose utilization ability. The domesticated strains from different niches generally form distinct lineages and harbor lineage-specific CNVs, HGTs and introgressions, which contribute to their adaptations to specific fermentation environments. However, whether the domesticated lineages originated from a single, or multiple domestication events is still hotly debated and the mechanism causing the diversification of the wild lineages remains to be illuminated. Further worldwide investigations on both wild and domesticated
, especially in Africa and West Asia, will be helpful for a better understanding of the natural and domestication histories and evolution of
.
Heterosis or hybrid vigor is a common phenomenon in plants and animals; however, the molecular mechanisms underlying heterosis remain elusive, despite extensive studies on the phenomenon for more ...than a century. Here we constructed a large collection of F1 hybrids of
by spore-to-spore mating between homozygous wild strains of the species with different genetic distances and compared growth performance of the F1 hybrids with their parents. We found that heterosis was prevalent in the F1 hybrids at 40°C. A hump-shaped relationship between heterosis and parental genetic distance was observed. We then analyzed transcriptomes of selected heterotic and depressed F1 hybrids and their parents growing at 40°C and found that genes associated with one-carbon metabolism and related pathways were generally up-regulated in the heterotic F1 hybrids, leading to improved cellular redox homeostasis at high temperature. Consistently, genes related with DNA repair, stress responses, and ion homeostasis were generally down-regulated in the heterotic F1 hybrids. Furthermore, genes associated with protein quality control systems were also generally down-regulated in the heterotic F1 hybrids, suggesting a lower level of protein turnover and thus higher energy use efficiency in these strains. In contrast, the depressed F1 hybrids, which were limited in number and mostly shared a common aneuploid parental strain, showed a largely opposite gene expression pattern to the heterotic F1 hybrids. We provide new insights into molecular mechanisms underlying heterosis and thermotolerance of yeast and new clues for a better understanding of the molecular basis of heterosis in plants and animals.
In this paper, the nonlinear differential equation for temperature distribution of convective straight fins with temperature-dependent thermal conductivity is solved by using a new modified ...decomposition method (MDM) for boundary value problems. In the new MDM the recursion scheme of the solution components does not involve any undetermined coefficients. Using the new method, the temperature distribution and the efficiency of the fin can be expressed analytically as functions containing two fin parameters without any undetermined coefficients, which greatly facilitates parameter analysis.
The space-fractional Fokker–Planck type equation ∂p∂t+γ∂p∂x=-D(-Δ)α/2p(0<α⩽2) subject to the initial condition p(x,0)=δ(x) is solved in terms of Fox H functions. The solution as γ=0 expresses the ...Lévy stable distribution with the index α. From the properties of Fox H functions, the series representation and asymptotic behavior for the solution are also obtained. Lévy stable distribution as 0<α<2 describes anomalous superdiffusion and its diffusion velocity is characterized by xd∝(Dt)1/α.
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