Four years of post-genomic life with 6,000 yeast genes

Optimization of a hybrid bacterial/Arabidopsis thaliana fatty acid synthase system II in Saccharomyces cerevisiae

Fatty acids are produced by eukaryotes like baker's yeast Saccharomyces cerevisiae mainly using a large multifunctional type I fatty acid synthase (FASI) where seven catalytic steps and a carrier domain are shared between one or two protein subunits. While this system may offer efficiency in catalysis, only a narrow range of fatty acids are produced. Prokaryotes, chloroplasts and mitochondria rely instead on a FAS type II (FASII) where each catalytic step is carried out by a monofunctional enzyme encoded by a separate gene. FASII is more flexible and capable of producing a wider range of fatty acid structures, such as the direct production of unsaturated fatty acids. An efficient FASII in the preferred industrial organism S. cerevisiae could provide a platform for developing sustainable production of specialized fatty acids. We functionally replaced either yeast FASI genes (FAS1 or FAS2) with a FASII consisting of nine genes from Escherichia coli (acpP, acpS and fab -A, -B, -D, -F, -G, -H, -Z) as well as three from Arabidopsis thaliana (MOD1, FATA1 and FATB). The genes were expressed from an autonomously replicating multicopy vector assembled using the Yeast Pathway Kit for in-vivo assembly in yeast. Two rounds of adaptation led to a strain with a maximum growth rate (μmax) of 0.19 h^-1 without exogenous fatty acids, twice the growth rate previously reported for a comparable strain. Additional copies of the MOD1 or fabH genes resulted in cultures with higher final cell densities and three times higher lipid content compared to the control.

High throughput mutagenesis and screening for yeast engineering

The eukaryotic yeast Saccharomyces cerevisiae is a model host utilized for whole cell biocatalytic conversions, protein evolution, and scientific inquiries into the pathogenesis of human disease. Over the past decade, the scale and pace of such studies has drastically increased alongside the advent of novel tools for both genome-wide studies and targeted genetic mutagenesis. In this review, we will detail past and present (e.g., CRISPR/Cas) genome-scale screening platforms, typically employed in the context of growth-based selections for improved whole cell phenotype or for mechanistic interrogations. We will further highlight recent advances that enable the rapid and often continuous evolution of biomolecules with improved function. Additionally, we will detail the corresponding advances in high throughput selection and screening strategies that are essential for assessing or isolating cellular and protein improvements. Finally, we will describe how future developments can continue to advance yeast high throughput engineering.

Promising advancement in fermentative succinic acid production by yeast hosts

As a platform chemical with various applications, succinic acid (SA) is currently produced by petrochemical processing from oil-derived substrates such as maleic acid. In order to replace the environmental unsustainable hydrocarbon economy with a renewable environmentally sound carbohydrate economy, bio-based SA production process has been developed during the past two decades. In this review, recent advances in the valorization of solid organic wastes including mixed food waste, agricultural waste and textile waste for efficient, green and sustainable SA production have been reviewed. Firstly, the application, market and key global players of bio-SA are summarized. Then achievements in SA production by several promising yeasts including Saccharomyces cerevisiae and Yarrowia lipolytica are detailed, followed by calculation and comparison of SA production costs between oil-based substrates and raw materials. Lastly, challenges in engineered microorganisms and fermentation processes are presented together with perspectives on the development of robust yeast SA producers via genome-scale metabolic optimization and application of low-cost raw materials as fermentation substrates. This review provides valuable insights for identifying useful directions for future bio-SA production improvement.

Cellular models of Batten disease

The Neuronal Ceroid Lipofuscinoses (NCL), otherwise known as Batten disease, are a group of neurodegenerative diseases caused by mutations in 13 known genes. All except one NCL is autosomal recessive in inheritance, with similar aetiology and characterised by the accumulation of autofluorescent storage material in the lysosomes of cells. Age of onset and the rate of progression vary between the NCLs. They are collectively one of the most common lysosomal storage diseases, but the enigma remains of how genetically distinct diseases result in such remarkably similar pathogenesis. Much has been learnt from cellular studies about the function of the proteins encoded by the affected genes. Such research has utilised primitive unicellular models such as yeast and amoeba containing gene orthologues, cells derived from naturally occurring (sheep) and genetically engineered (mouse) animal models or patient-derived cells. Most recently, patient-derived induced pluripotent stem cell (iPSC) lines have been differentiated into neural cell-types to study molecular pathogenesis in the cells most profoundly affected by disease. Here, we review how cell models have informed much of the biochemical understanding of the NCLs and how more complex models are being used to further this understanding and potentially act as platforms for therapeutic efficacy studies in the future.

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Developments made in cellular models for neuronal ceroid lipofuscinosis (NCL) in basic biology and use as therapeutic platforms.

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Cellular models elucidating function of NCL proteins.

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NCL proteins implicated in the mTor signalling pathway.

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Patient-derived induced pluripotent stem cell (iPSC) lines have been differentiated into neural cell-types providing insights into the molecular pathogenesis of NCL.

Biocompatibility assessment of single-walled carbon nanotubes using Saccharomyces cerevisiae as a model organism

BACKGROUND

Single-walled carbon nanotubes (SWCNTs) have many potential applications in various fields. Especially, the unique physicochemical properties make them as the prime candidates for applications in biomedical fields. However, biocompatibility of SWCNTs has been a major concern for their applications. In the study, biocompatibility of oxidized SWCNTs (O-SWCNTs) was assessed using Saccharomyces cerevisiae (S. cerevisiae) as a model organism.

RESULTS

Cell proliferation and viability were significantly changed after exposure to O-SWCNTs (188.2 and 376.4 mg/L) for 24 h. O-SWCNTs were internalized in cells and distributed in cytoplasm, vesicles, lysosomes and cell nucleus. The average O-SWCNTs contents in S. cerevisiae were ranged from 0.18 to 4.82 mg/g during the exposure from 0 to 24 h, and the maximum content was reached at 18 h after exposure. Both penetration and endocytosis were involved in the internalization of O-SWCNTs in S. cerevisiae, and endocytosis was the main pathway. Cellular structures and morphology were changed after exposure to O-SWCNTs, such as undulating appearance at the membrane, shrinking of the cytosol, increased numbers of lipid droplets and disruption of vacuoles. ROS and antioxidant enzymes activities were observably changed following exposure. For the treatment at 376.4 mg/L, 20.8% of the total cells was undergone apoptosis. Decrease of mitochondrial transmembrane potential and leakage of cytochrome c from mitochondria were observed after exposure. Moreover, expression levels of apoptosis-related genes were significantly increased.

CONCLUSIONS

O-SWCNTs can internalize in S. cerevisiae cells via direct penetration and endocytosis, and distribute in cytoplasm, vesicles, lysosomes and cell nucleus. Besides, O-SWCNTs (188.2 and 376.4 mg/L) can induce apoptosis in S. cerevisiae cells, and oxidative stress is involved in activation of the mitochondria-dependent apoptotic pathway.

Using Barcoded HIV Ensembles (B-HIVE) for Single Provirus Transcriptomics

The latent HIV reservoir is the main barrier to curing AIDS, because infected cells escape the immune system and antiretroviral therapies. Developing new treatment strategies requires technologies to trace latent proviruses. Here, we describe a genome-wide technique called Barcoded HIV Ensembles (B-HIVE) to measure HIV expression at the single provirus level. The principle of B-HIVE is to tag the genome of HIV with DNA barcodes to trace viral transcripts produced by single proviruses in an infected cell population. This in turn reveals which proviruses are active and which are latent or expressed at low level. B-HIVE is a high-throughput method to identify and quantify thousands of individual viral transcripts per round of infection. It can be applied in different conditions, characterizing the response of single proviruses to different treatments. Overall, B-HIVE gives unprecedented insight into the expression of single proviruses in populations of HIV-infected cells. © 2018 by John Wiley & Sons, Inc.

Transcriptomic analysis of thermotolerant yeastKluyveromyces marxianusin multiple inhibitors tolerance

Global transcriptional response ofK. marxianusto multiple inhibitors including acetic acid, phenols, furfural and HMF at 42 °C.

Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data

Since its original inception over 150 years ago by Darwin, we have made tremendous progress toward the reconstruction of the Tree of Life. In particular, the transition from analyzing datasets comprised of small numbers of loci to those comprised of hundreds of loci, if not entire genomes, has aided in resolving some of the most vexing of evolutionary problems while giving us a new perspective on biodiversity. Correspondingly, phylogenetic trees have taken a central role in fields that span ecology, conservation, and medicine. However, the rise of big data has also presented phylogenomicists with a new set of challenges to experimental design, quantitative analyses, and computation. The sequencing of a number of very first genomes presented significant challenges to phylogenetic inference, leading fungal phylogenomicists to begin addressing pitfalls and postulating solutions to the issues that arise from genome-scale analyses relevant to any lineage across the Tree of Life. Here we highlight insights from fungal phylogenomics for topics including systematics and species delimitation, ecological and phenotypic diversification, and biogeography while providing an overview of progress made on the reconstruction of the fungal Tree of Life. Finally, we provide a review of considerations to phylogenomic experimental design for robust tree inference. We hope that this special issue of Advances in Genetics not only excites the continued progress of fungal evolutionary biology but also motivates the interdisciplinary development of new theory and methods designed to maximize the power of genomic scale data in phylogenetic analyses.

Mitochondrial impairment and oxidative stress mediated apoptosis induced by α-Fe2O3 nanoparticles in Saccharomyces cerevisiae

In this study, the potential toxicity of α-Fe2O3-NPs was investigated using a unicellular eukaryote model, Saccharomyces cerevisiae (S. cerevisiae). The results showed that cell viability and proliferation were significantly decreased (p < 0.01) following exposure to 100-600 mg L-1 for 24 h. The IC50 and LC50 values were 352 and 541 mg L-1, respectively. Toxic effects were attributed to α-Fe2O3-NPs rather than iron ions released from the NPs. α-Fe2O3-NPs were accumulated in the vacuole and cytoplasm, and the maximum accumulation (3.95 mg g-1) was reached at 12 h. About 48.6% of cells underwent late apoptosis/necrosis at 600 mg L-1, and the mitochondrial transmembrane potential was significantly decreased (p < 0.01) at 50-600 mg L-1. Biomarkers of oxidative stress [reactive oxygen species (ROS), superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPx)] and the expression of apoptosis-related genes (Yca1, Nma111, Nuc1 and SOD) were significantly changed after exposure. These combined results indicated that α-Fe2O3-NPs were rapidly internalized in S. cerevisiae, and the accumulated NPs induced cell apoptosis mediated by mitochondrial impairment and oxidative stress.

Toxicological effects of graphene oxide on Saccharomyces cerevisiae

Using Saccharomyces cerevisiae as an experimental model, the potential toxicity of graphene oxide (GO) was evaluated following exposure to 0-600 mg L-1 for 24 h. The results showed that cell proliferation was observably inhibited and the IC50 value was 352.704 mg L-1. Mortality showed a concentration-dependent increase, and was 19.3% at 600 mg L-1. A small number of cells were deformed and shrunken after exposure. The percentage of late apoptosis/necrosis showed a significant increase (p < 0.01) at 600 mg L-1 (19.16%) compared with the control (1.14%). The mitochondrial transmembrane potential was significantly decreased (p < 0.01) at 50-600 mg L-1, indicating that the apoptosis was related to mitochondrial impairment. Moreover, ROS was observably increased (p < 0.01) at 200, 400 and 600 mg L-1. The expressions of apoptosis-related genes (SOD, Yca1, Nma111 and Nuc1) were significantly changed. The results presented so far indicate that GO has the potential to cause adverse effects on organisms when released into the environment.

Toxicological effects of multi-walled carbon nanotubes on Saccharomyces cerevisiae: The uptake kinetics and mechanisms and the toxic responses

Using Saccharomyces cerevisiae as an experimental model, the potential toxicological effects of oxidized multi-walled carbon nanotubes (MWCNTs) were investigated following exposure to 0-600mg/L for 24h. Results indicated that MWCNTs (>100mg/L) had adverse effects on the cell proliferation. MWCNTs were clearly visible in lysosome, vacuole, endosome, mitochondria, multivesicular body and localization in the perinuclear region. The uptake kinetics data demonstrated that the maximum MWCNTs content (209.61mg/g) was reached at 3h, and a steady state was reached after 18h. Based on the combined results of transmission electron microscope, endocytosis inhibition experiments and endocytosis-related genes (END3, END6, Sla2 and Rsp5) expression analysis, we elucidated MWCNTs uptake mechanism: (i) via a direct penetration of single MWCNTs; (ii) via endocytosis of single MWCNTs; and (iii) via endocytosis of MWCNTs aggregates. The percentage of apoptosis was significant increased at 600mg/L. The decrease of mitochondrial transmembrane potential and the leakage of cytochrome c shown dose-dependent manners. Interestingly, there was no significant increase of reactive oxygen species (ROS). The apoptosis-related genes (SOD1, SOD2, Yca1, Nma111 and Nuc1) were significant changed. These results obtained in our study demonstrated that oxidized MWCNTs induce Saccharomyces cerevisiae apoptosis via mitochondrial impairment pathway.

Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC)

Background

Genomes of E. coli, including that of the human pathogen Escherichia coli O157:H7 (EHEC) EDL933, still harbor undetected protein-coding genes which, apparently, have escaped annotation due to their small size and non-essential function. To find such genes, global gene expression of EHEC EDL933 was examined, using strand-specific RNAseq (transcriptome), ribosomal footprinting (translatome) and mass spectrometry (proteome).

Results

Using the above methods, 72 short, non-annotated protein-coding genes were detected. All of these showed signals in the ribosomal footprinting assay indicating mRNA translation. Seven were verified by mass spectrometry. Fifty-seven genes are annotated in other enterobacteriaceae, mainly as hypothetical genes; the remaining 15 genes constitute novel discoveries. In addition, protein structure and function were predicted computationally and compared between EHEC-encoded proteins and 100-times randomly shuffled proteins. Based on this comparison, 61 of the 72 novel proteins exhibit predicted structural and functional features similar to those of annotated proteins. Many of the novel genes show differential transcription when grown under eleven diverse growth conditions suggesting environmental regulation. Three genes were found to confer a phenotype in previous studies, e.g., decreased cattle colonization.

Conclusions

These findings demonstrate that ribosomal footprinting can be used to detect novel protein coding genes, contributing to the growing body of evidence that hypothetical genes are not annotation artifacts and opening an additional way to study their functionality. All 72 genes are taxonomically restricted and, therefore, appear to have evolved relatively recently de novo.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2456-1) contains supplementary material, which is available to authorized users.

The neuronal ceroid lipofuscinoses: Opportunities from model systems

The neuronal ceroid lipofuscinoses are a group of severe and progressive neurodegenerative disorders, generally with childhood onset. Despite the fact that these diseases remain fatal, significant breakthroughs have been made in our understanding of the genetics that underpin these conditions. This understanding has allowed the development of a broad range of models to study disease processes, and to develop new therapeutic approaches. Such models have contributed significantly to our knowledge of these conditions. In this review we will focus on the advantages of each individual model, describe some of the contributions the models have made to our understanding of the broader disease biology and highlight new techniques and approaches relevant to the study and potential treatment of the neuronal ceroid lipofuscinoses. This article is part of a Special Issue entitled: "Current Research on the Neuronal Ceroid Lipofuscinoses (Batten Disease)".

Functional study of the Hap4-like genes suggests that the key regulators of carbon metabolism HAP4 and oxidative stress response YAP1 in yeast diverged from a common ancestor

The transcriptional regulator HAP4, induced by respiratory substrates, is involved in the balance between fermentation and respiration in S. cerevisiae. We identified putative orthologues of the Hap4 protein in all ascomycetes, based only on a conserved sixteen amino acid-long motif. In addition to this motif, some of these proteins contain a DNA-binding motif of the bZIP type, while being nonetheless globally highly divergent. The genome of the yeast Hansenula polymorpha contains two HAP4-like genes encoding the protein HpHap4-A which, like ScHap4, is devoid of a bZIP motif, and HpHap4-B which contains it. This species has been chosen for a detailed examination of their respective properties. Based mostly on global gene expression studies performed in the S. cerevisiae HAP4 disruption mutant (ScΔhap4), we show here that HpHap4-A is functionally equivalent to ScHap4, whereas HpHap4-B is not. Moreover HpHAP4-B is able to complement the H₂O₂ hypersensitivity of the ScYap1 deletant, YAP1 being, in S. cerevisiae, the main regulator of oxidative stress. Finally, a transcriptomic analysis performed in the ScΔyap1 strain overexpressing HpHAP4-B shows that HpHap4-B acts both on oxidative stress response and carbohydrate metabolism in a manner different from both ScYap1 and ScHap4. Deletion of these two genes in their natural host, H. polymorpha, confirms that HpHAP4-A participates in the control of the fermentation/respiration balance, while HpHAP4-B is involved in oxidative stress since its deletion leads to hypersensitivity to H₂O₂. These data, placed in an evolutionary context, raise new questions concerning the evolution of the HAP4 transcriptional regulation function and suggest that Yap1 and Hap4 have diverged from a unique regulatory protein in the fungal ancestor.

Genomic insights into the evolution of industrial yeast species Brettanomyces bruxellensis

Brettanomyces bruxellensis, like its wine yeast counterpart Saccharomyces cerevisiae, is intrinsically linked with industrial fermentations. In wine, B. bruxellensis is generally considered to contribute negative influences on wine quality, whereas for some styles of beer, it is an essential contributor. More recently, it has shown some potential for bioethanol production. Our relatively poor understanding of B. bruxellensis biology, at least when compared with S. cerevisiae, is partly due to a lack of laboratory tools. As it is a nonmodel organism, efforts to develop methods for sporulation and transformation have been sporadic and largely unsuccessful. Recent genome sequencing efforts are now providing B. bruxellensis researchers unprecedented access to gene catalogues, the possibility of performing transcriptomic studies and new insights into evolutionary drivers. This review summarises these findings, emphasises the rich data sets already available yet largely unexplored and looks over the horizon at what might be learnt soon through comprehensive population genomics of B. bruxellensis and related species.

The yeast deletion collection: a decade of functional genomics

The yeast deletion collections comprise >21,000 mutant strains that carry precise start-to-stop deletions of ∼6000 open reading frames. This collection includes heterozygous and homozygous diploids, and haploids of both MATa and MATα mating types. The yeast deletion collection, or yeast knockout (YKO) set, represents the first and only complete, systematically constructed deletion collection available for any organism. Conceived during the Saccharomyces cerevisiae sequencing project, work on the project began in 1998 and was completed in 2002. The YKO strains have been used in numerous laboratories in >1000 genome-wide screens. This landmark genome project has inspired development of numerous genome-wide technologies in organisms from yeast to man. Notable spinoff technologies include synthetic genetic array and HIPHOP chemogenomics. In this retrospective, we briefly describe the yeast deletion project and some of its most noteworthy biological contributions and the impact that these collections have had on the yeast research community and on genomics in general.

Towards defining the substrate of orphan P5A-ATPases

BACKGROUND

P-type ATPases are ubiquitous ion and lipid pumps found in cellular membranes. P5A-ATPases constitute a poorly characterized subfamily of P-type ATPases present in all eukaryotic organisms but for which a transported substrate remains to be identified.

SCOPE OF REVIEW

This review aims to discuss the available evidence which could lead to identification of possible substrates of P5A-ATPases.

MAJOR CONCLUSIONS

The complex phenotypes resulting from the loss of P5A-ATPases in model organisms can be explained by a role of the P5A-ATPase in the endoplasmic reticulum (ER), where loss of function leads to broad and unspecific phenotypes related to the impairment of basic ER functions such as protein folding and processing. Genetic interactions in Saccharomyces cerevisiae point to a role of the endogenous P5A-ATPase Spf1p in separation of charges in the ER, in sterol metabolism, and in insertion of tail-anchored proteins in the ER membrane. A role for P5A-ATPases in vesicle formation would explain why sterol transport and distribution are affected in knock out cells, which in turn has a negative impact on the spontaneous insertion of tail-anchored proteins. It would also explain why secretory proteins destined for the Golgi and the cell wall have difficulties in reaching their final destination. Cations and phospholipids could both be transported substrates of P5A-ATPases and as each carry charges, transport of either might explain why a charge difference arises across the ER membrane.

GENERAL SIGNIFICANCE

Identification of the substrate of P5A-ATPases would throw light on an important general process in the ER that is still not fully understood. This article is part of a Special Issue entitled Structural biochemistry and biophysics of membrane proteins.

The impact of proteomics on the understanding of functions and biogenesis of fungal extracellular vesicles

Several microbial molecules are released to the extracellular space in vesicle-like structures. In pathogenic fungi, these molecules include pigments, polysaccharides, lipids, and proteins, which traverse the cell wall in vesicles that accumulate in the extracellular space. The diverse composition of fungal extracellular vesicles (EV) is indicative of multiple mechanisms of cellular biogenesis, a hypothesis that was supported by EV proteomic studies in a set of Saccharomyces cerevisiae strains with defects in both conventional and unconventional secretory pathways. In the human pathogens Cryptococcus neoformans, Histoplasma capsulatum, and Paracoccidioides brasiliensis, extracellular vesicle proteomics revealed the presence of proteins with both immunological and pathogenic activities. In fact, fungal EV have been demonstrated to interfere with the activity of immune effector cells and to increase fungal pathogenesis. In this review, we discuss the impact of proteomics on the understanding of functions and biogenesis of fungal EV, as well as the potential role of these structures in fungal pathogenesis. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.

Utilization of Saccharomyces cerevisiae recombinant strain incapable of both ethanol and glycerol biosynthesis for anaerobic bioproduction

The yeast Saccharomyces cerevisiae produces ethanol and glycerol as major unwanted byproducts, unless ethanol and glycerol are the target compounds. Minimizing the levels of these byproducts is important for bioproduction processes using yeast cells. In this study, we constructed a yeast strain in which both ethanol and glycerol production pathways were disrupted and examined its culture characteristics. In wild-type yeast strain, metabolic pathways that produce ethanol and glycerol play an important role in reoxidizing nicotinamide adenine dinucleotide (NADH) generated during glycolysis, particularly under anaerobic conditions. Strains in which both pathways were disrupted therefore failed to grow and consume glucose under anaerobic conditions. Introduction of desired metabolic reaction(s) coupled with NADH oxidation enabled the engineered strain to consume substrate and produce target compound(s). Here we introduced NADH-oxidization-coupled L-lactate production mechanisms into a yeast strain incapable of ethanol and glycerol biosynthesis, based on in silico simulation using a genome-scale metabolic model of S. cerevisiae. From the results of in silico simulation based on flux balance analysis, a feasible anaerobic non-growing metabolic state, in which L-lactate yield approached the theoretical maximum, was identified and this phenomenon was verified experimentally. The yeast strain incapable of both ethanol and glycerol biosynthesis is a potentially valuable host for bioproduction coupled with NADH oxidation under anaerobic conditions.

Engineering of acetyl-CoA metabolism for the improved production of polyhydroxybutyrate in Saccharomyces cerevisiae

Through metabolic engineering microorganisms can be engineered to produce new products and further produce these with higher yield and productivities. Here, we expressed the bacterial polyhydroxybutyrate (PHB) pathway in the yeast Saccharomyces cerevisiae and we further evaluated the effect of engineering the formation of acetyl coenzyme A (acetyl-CoA), an intermediate of the central carbon metabolism and precursor of the PHB pathway, on heterologous PHB production by yeast. We engineered the acetyl-CoA metabolism by co-transformation of a plasmid containing genes for native S. cerevisiae alcohol dehydrogenase (ADH2), acetaldehyde dehydrogenase (ALD6), acetyl-CoA acetyltransferase (ERG10) and a Salmonella enterica acetyl-CoA synthetase variant (acsL641P), resulting in acetoacetyl-CoA overproduction, together with a plasmid containing the PHB pathway genes coding for acetyl-CoA acetyltransferase (phaA), NADPH-linked acetoacetyl-CoA reductase (phaB) and poly(3-hydroxybutyrate) polymerase (phaC) from Ralstonia eutropha H16. Introduction of the acetyl-CoA plasmid together with the PHB plasmid, improved the productivity of PHB more than 16 times compared to the reference strain used in this study, as well as it reduced the specific product formation of side products.

Reconstruction of cytosolic fumaric acid biosynthetic pathways in Saccharomyces cerevisiae

Background

Fumaric acid is a commercially important component of foodstuffs, pharmaceuticals and industrial materials, yet the current methods of production are unsustainable and ecologically destructive.

Results

In this study, the fumarate biosynthetic pathway involving reductive reactions of the tricarboxylic acid cycle was exogenously introduced in S. cerevisiae by a series of simple genetic modifications. First, the Rhizopus oryzae genes for malate dehydrogenase (RoMDH) and fumarase (RoFUM1) were heterologously expressed. Then, expression of the endogenous pyruvate carboxylase (PYC2) was up-regulated. The resultant yeast strain, FMME-001 ↑PYC2 + ↑RoMDH, was capable of producing significantly higher yields of fumarate in the glucose medium (3.18 ± 0.15 g liter^-1) than the control strain FMME-001 empty vector.

Conclusions

The results presented here provide a novel strategy for fumarate biosynthesis, which represents an important advancement in producing high yields of fumarate in a sustainable and ecologically-friendly manner.

Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors

We propose a method to predict yeast transcription factor targets by integrating histone modification profiles with transcription factor binding motif information. It shows improved predictive power compared to a binding motif-only method. We find that transcription factors cluster into histone-sensitive and -insensitive classes. The target genes of histone-sensitive transcription factors have stronger histone modification signals than those of histone-insensitive ones. The two classes also differ in tendency to interact with histone modifiers, degree of connectivity in protein-protein interaction networks, position in the transcriptional regulation hierarchy, and in a number of additional features, indicating possible differences in their transcriptional regulation mechanisms.

Subcellular shotgun proteomics in plants: looking beyond the usual suspects

In this review we examine the current state of analytical methods used for shotgun proteomics experiments in plants. The rapid advances in this field in recent years are discussed, and contrasted with experiments performed using current widely used procedures. We also examine the use of subcellular fractionation approaches as they apply to plant proteomics, and discuss how appropriate sample preparation can produce a great increase in proteome coverage in subsequent analysis. We conclude that the conjunction of these two techniques represents a significant advance in plant proteomics, and the future of plant biology research will continue to be enriched by the ongoing development of proteomic analytical technology.

KlRHO1 and KlPKC1 are essential for cell integrity signalling in Kluyveromyces lactis

Cell integrity in yeasts is ensured by a rigid cell wall whose synthesis is triggered by a MAP kinase-mediated signal-transduction cascade. Upstream regulatory components of this pathway inSaccharomyces cerevisiaeinvolve a single protein kinase C, which is regulated by interaction with the small GTPase Rho1. Here, two genes were isolated which encode these proteins fromKluyveromyces lactis(KlPKC1andKlRHO1). Sequencing showed ORFs which encode proteins of 1161 and 208 amino acids, respectively. The deduced proteins shared 59 and 85 % overall amino acid identities, respectively, with their homologues fromS. cerevisiae. Null mutants in both genes were non-viable, as shown by tetrad analyses of the heterozygous diploid strains. Overexpression of theKlRHO1gene under the control of theScGAL1promoter severely impaired growth in bothS. cerevisiaeandK. lactis. On the other hand, a similar construct withKlPKC1did not show a pronounced phenotype. Two-hybrid analyses showed interaction between Rho1 and Pkc1 for theK. lactisproteins and theirS. cerevisiaehomologues. A green fluorescent protein (GFP) fusion to the C-terminal end of KlPkc1 located the protein to patches in the growing bud, and at certain stages of the division process also to the bud neck. N-terminal GFP fusions to KlRho1 localized mainly to the cell surface (presumably the cytoplasmic side of the plasma membrane) and to the vacuole, with some indications of traffic from the former to the latter. Thus, KlPkc1 and KlRho1 have been shown to serve vital functions inK. lactis, to interact in cell integrity signalling and to traffic between the plasma membrane and the vacuole.

Hybridization monitor: A method for identifying differences between complex genomes

We have developed a method to identify and amplify differential fragments between two complex genomes. This technique, named hybridization-monitored genome differential analysis (HMDA), incorporates a monitor system into a PCR-based solid subtraction hybridization that tracks the entire hybridization process. This is achieved by monitoring the subtraction progress using PCR analysis of the conserved sequence of 18S rDNA in the tester sample after each round of subtraction. Homologous fragments can then be eliminated when bound to the driver DNA immobilized on a solid membrane. The hybridization continues until the conserved DNA sequence of 18S rDNA can no longer be detected, and most of the unbound DNA fragments left in the liquid were mainly the tester-specific fragments, thus greatly decreasing the complexity of DNA template of PCR amplification, increasing the amplification efficiency of differences accordingly, and ensuring high positive efficiency and coverage across the tester genome. We have applied the technique in a comparison between the genomes of Saccharomyces cerevisiae and Schizosaccharomyces pombe, which are two completely sequenced organisms. Results indicated that 95% of the subtracted clones have been confirmed to be different to the driver analyzed using the BLASTN homology alignment. With this technique, 240-fold enrichment of differences is obtained, and the coverage of the difference is up to 79%. These results indicate that HMDA can efficiently identify sequences that differ between two complex genomes.

Coupling the Immobilized Trypsin Microreactor of Monolithic Capillary with μRPLC−MS/MS for Shotgun Proteome Analysis

A nanoliter trypsin-based monolithic microreactor coupled with muRPLC-MS/MS was reported for shotgun proteome analysis. The proteins were rapidly digested by the microreactor, and the resulting protein digests were directly loaded onto a muRPLC column for separation followed with detection of the eluted peptides by tandem mass spectrometer. The digestion efficiency and stability of the microreactor was demonstrated by using bovine serum albumin as a model protein. When compared with an incubation time of more than 10 h by free trypsin in the conventional digestion approach, protein mixtures can be digested by the microreactor in several minutes. This system was applied to the analysis of the total cell lysate of Saccharomyces cerevisiae. After a Sequest database search, a total of 1578 unique peptides corresponding to 541 proteins were identified when 590 ng yeast protein was digested by the microreactor with an incubation time of only 1 min.

Comprehensive proteomics in yeast using chromatographic fractionation, gas phase fractionation, protein gel electrophoresis, and isoelectric focusing

We have investigated the use of a variety of different techniques to identify as many proteins as possible in a yeast lysate, with the aim of investigating the overlap and complementarity of data from different approaches. A standard lysate was prepared from log phase yeast (Saccharomyces cerevisiae). This was then subjected to analysis via five different approaches aimed at identifying as many proteins as possible using an ion trap mass spectrometer. The total number of non-redundant protein identifications from each experiment was: 524 proteins by 2-D (SCX/C18) nanoflow liquid chromatography-liquid chromatography tandem mass spectrometry (nanoLC-LC MS/MS (MudPIT)); 381 proteins by nanoLC-MS/MS with gas phase fractionation by mass range selection; 390 proteins by nanoLC-MS/MS with gas phase fractionation by ion abundance selection; 898 proteins by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) separation of proteins, in-gel digestion, and nanoLC-MS/MS of gel slices; and 422 proteins by isoelectric focusing of proteins, in-gel digestion and nanoLC-MS/MS of gel slices. The total number of non-redundant protein identifications in the five experiments was 1204. Combining only the two best experiments, the SDS-PAGE gel slices and the Mudpit, produces 1024 proteins identified, more than 85% of the total. Clearly, combining a Mudpit analysis with an SDS-PAGE gel slice experiment gives the greatest amount of protein identification information from a limited amount of sample.

Homofermentative lactate production cannot sustain anaerobic growth of engineered Saccharomyces cerevisiae: possible consequence of energy-dependent lactate export

Due to a growing market for the biodegradable and renewable polymer polylactic acid, the world demand for lactic acid is rapidly increasing. The tolerance of yeasts to low pH can benefit the process economy of lactic acid production by minimizing the need for neutralizing agents. Saccharomyces cerevisiae (CEN.PK background) was engineered to a homofermentative lactate-producing yeast via deletion of the three genes encoding pyruvate decarboxylase and the introduction of a heterologous lactate dehydrogenase (EC 1.1.1.27). Like all pyruvate decarboxylase-negative S. cerevisiae strains, the engineered strain required small amounts of acetate for the synthesis of cytosolic acetyl-coenzyme A. Exposure of aerobic glucose-limited chemostat cultures to excess glucose resulted in the immediate appearance of lactate as the major fermentation product. Ethanol formation was absent. However, the engineered strain could not grow anaerobically, and lactate production was strongly stimulated by oxygen. In addition, under all conditions examined, lactate production by the engineered strain was slower than alcoholic fermentation by the wild type. Despite the equivalence of alcoholic fermentation and lactate fermentation with respect to redox balance and ATP generation, studies on oxygen-limited chemostat cultures showed that lactate production does not contribute to the ATP economy of the engineered yeast. This absence of net ATP production is probably due to a metabolic energy requirement (directly or indirectly in the form of ATP) for lactate export.

Cyanobacterial postgenomic research and systems biology

The genomic era brought with it the capacity to unlock complex interactions in organisms and biological systems. Currently, by exploiting genomic and associated protein information through in silico analyses, postgenomic research is developing rapidly. This field, which encompasses functional genomics, structural genomics, transcriptomics, pharmacogenomics, proteomics and metabolomics, allows for a systems-wide approach to biological studies. To date, bacterial postgenomic research has focused mainly on a few representative pathogenic species, leaving the vast majority of the microbial community relatively overlooked. Amongst the under-represented microorganisms are the cyanobacteria, which are important for their beneficial natural product production, bioremediation and energy applications. Here, we highlight the current status of cyanobacterial postgenomic research and assess the potential for future metabolic engineering and "cell factory" or "microbial cell" development.

The uses of genome-wide yeast mutant collections

We assess five years of usage of the major genome-wide collections of mutants from Saccharomyces cerevisiae: single deletion mutants, double mutants conferring 'synthetic' lethality and the 'TRIPLES' collection of mutants obtained by random transposon insertion. Over 100 experimental conditions have been tested and more than 5,000 novel phenotypic traits have been assigned to yeast genes using these collections.

Comparative genotyping of the Saccharomyces cerevisiae laboratory strains S288C and CEN.PK113-7D using oligonucleotide microarrays

To analyse the reliability and accuracy of genotype analysis with high-density oligonucleotide microarrays, this method and other experimental approaches were used to analyse genomic DNA of two popular Saccharomyces cerevisiae laboratory strains. S288C was used for systematic sequencing of 'the' S. cerevisiae genome; CEN.PK113-7D is a popular strain for physiological studies and functional genomics. Random amplified polymorphic DNA, electrophoretic karyotyping and microarray analysis all indicated a high level of sequence similarity between the two strains. In the microarray analysis, as few as 288 (4.5%) of the ca. 6300 represented yeast genes were identified that yielded significantly different hybridisation intensities between the two strains. These could be classified as amplified, absent, or with sequence polymorphism in CEN.PK113-7D compared to S288C. A detailed analysis focused on the subset of 25 genes called absent in CEN.PK113-7D. Among these absent genes, 17 were clustered together on five chromosomes, mainly in subtelomeric regions. Thorough analysis of these regions by polymerase chain reaction (PCR) and restriction fragment length polymorphism confirmed the absence of these genes in CEN.PK113-7D. Surprisingly, three of these regions were not smaller in CEN.PK113-7D chromosomes, indicating that they may harbour unidentified and potentially new sequences. In addition, eight genes called absent by the microarrays were scattered over the chromosomes. Using diagnostic PCR most of these genes were actually found to be present in CEN.PK113-7D, but after sequencing were found to differ significantly at the DNA level from S288C, explaining the poor hybridisation to the arrays. Our results indicate that DNA microarrays are a powerful tool for determining genotypic similarity between different yeast strains. However, to obtain meaningful information at the individual gene level, this method should be backed up by additional techniques.

Global analysis of protein expression in yeast

The availability of complete genomic sequences and technologies that allow comprehensive analysis of global expression profiles of messenger RNA have greatly expanded our ability to monitor the internal state of a cell. Yet biological systems ultimately need to be explained in terms of the activity, regulation and modification of proteins--and the ubiquitous occurrence of post-transcriptional regulation makes mRNA an imperfect proxy for such information. To facilitate global protein analyses, we have created a Saccharomyces cerevisiae fusion library where each open reading frame is tagged with a high-affinity epitope and expressed from its natural chromosomal location. Through immunodetection of the common tag, we obtain a census of proteins expressed during log-phase growth and measurements of their absolute levels. We find that about 80% of the proteome is expressed during normal growth conditions, and, using additional sequence information, we systematically identify misannotated genes. The abundance of proteins ranges from fewer than 50 to more than 10(6) molecules per cell. Many of these molecules, including essential proteins and most transcription factors, are present at levels that are not readily detectable by other proteomic techniques nor predictable by mRNA levels or codon bias measurements.

Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level

BACKGROUND

Genome projects have provided a vast amount of sequence information. Sequence comparison between species helps to establish functional catalogues within organisms and to study how they are maintained and modified across phylogenetic groups during evolution. Microarray studies allow us to determine groups of genes with similar temporal regulation and perhaps also common regulatory upstream regions for binding of transcription factors. The integration of sequence and expression data is expected to refine our current annotations and provide some insight into the evolution of gene regulation across organisms.

RESULTS

We have investigated how well the protein subcellular localization and functional categories established from clustering of orthologous genes agree with gene-expression data in Saccharomyces cerevisiae. An increase in the resolution of biologically meaningful classes is observed upon the combination of experiments under different conditions. The functional categories deduced by sequence comparison approaches are, in general, preserved at the level of expression and can sometimes interact into larger co-regulated networks, such as the protein translation process. Differences and similarities in the expression between cytoplasmic-mitochondrial and interspecies translation machineries complement evolutionary information from sequence similarity.

CONCLUSIONS

Combination of several microarray experiments is a powerful tool for the identification of upstream regulatory motifs of yeast genes involved in protein synthesis. Comparison of these yeast co-regulated genes against the archaeal and bacterial operons indicates that the components of the protein translation process are conserved across organisms at the expression level with minor specific adaptations.

Genetically modified industrial yeast ready for application

Tremendous progress in the genetic engineering of yeast had been achieved at the end of 20th century, including the complete genome sequence, genome-wide gene expression profiling, and whole gene disruption strains. Nevertheless, genetically modified (GM) baking, brewing, wine, and sake yeasts have not, as yet, been used commercially, although numerous industrial recombinant yeasts have been constructed. The recent progress of genetic engineering for the construction of GM yeast is reviewed and possible requirements for their application are discussed. 'Self-cloning' yeast will be the most likely candidate for the first commercial application of GM microorganisms in food and beverage industries.

The multidrug resistance transporters of the major facilitator superfamily, 6 years after disclosure of Saccharomyces cerevisiae genome sequence

The emergence of multidrug resistance (MDR) plays a crucial role in the failure of treatments of tumors and infectious diseases and in the control of plant pathogens, weeds and food-poisoning and food-spoilage microorganisms. Among the mechanisms underlying the MDR phenomenon in various organisms is the action of transmembrane transport proteins that presumably catalyse the active expulsion of structurally and functionally unrelated cytotoxic compounds out of the cell or their intracellular partitioning. On the basis of the complete genome sequence of Saccharomyces cerevisiae, numerous established and putative multidrug transporters were identified in this non-pathogenic, easy to manipulate eukaryotic model system. In yeast, the putative drug:H(+)-antiporters belong to the major facilitator superfamily; they comprise at least 23 proteins that have largely escaped characterisation by classical approaches. Other MDR determinants are membrane transporters belonging to the ATP binding cassette (ABC) superfamily, that utilize the energy of ATP hydrolysis for activity, and factors for transcriptional regulation of all the MDR transporters. This work reviews the current status of knowledge on the poorly characterized H(+)-antiporters, with 12 and 14 predicted spans, DHA12 and DHA14, drug efflux families. Consideration is given to the inventory and phylogenetic characterization, role as MDR determinants, regulation of gene expression, subcellular localisation and activity as solute transporters. Most of the present knowledge on these putative drug:H(+)-antiporters was driven by disclosure of S. cerevisiae genome sequence, in April 1996, being a paradigm of post-genomic research.

Saccharomyces cerevisiae resistance to chlorinated phenoxyacetic acid herbicides involves Pdr1p-mediated transcriptional activation of TPO1 and PDR5 genes

The transcription regulator Pdr1p is a determinant of Saccharomyces cerevisiae resistance to 2-methyl-4-chlorophenoxyacetic acid (MCPA) and 2,4-dichlorophenoxyacetic acid (2,4-D). The Pdr1p-regulated genes, TPO1 and PDR5, encoding putative multidrug transporters belonging to the major facilitator superfamily (MFS) and to the ATP-binding cassette (ABC) superfamily, respectively, are required for yeast resistance to sudden exposure to these herbicides. A rapid and transient activation of TPO1 (sixfold) and PDR5 (twofold) transcription takes place during the adaptation period preceding cell division under MCPA or 2,4-D moderate stress. These activations are mediated by both Pdr1p and Pdr3p and, as soon as adapted cells start duplication under herbicide stress, mRNA levels are drastically reduced to basal values. The longer duration of the adaptation period, observed for the Delta(pdr1) population, may involve the abolishment of the Pdr1p-mediated transcriptional activation of TPO1 and PDR5 genes, whose expression is critical to surpass the viability loss during the initial period of adaptation to the herbicides.

Large scale analysis of sequences from Neurospora crassa

After 50 years of analysing Neurospora crassa genes one by one large scale sequence analysis has increased the number of accessible genes tremendously in the last few years. Being the only filamentous fungus for which a comprehensive genomic sequence database is publicly accessible N. crassa serves as the model for this important group of microorganisms. The MIPS N. crassa database currently holds more than 16 Mb of non-redundant data of the chromosomes II and V analysed by the German Neurospora Genome Project. This represents more than one-third of the genome. Open reading frames (ORFs) have been extracted from the sequence and the deduced proteins have been annotated extensively. They are classified according to matches in sequence databases and attributed to functional categories according to their relatives. While 41% of analysed proteins are related to known proteins, 30% are hypothetical proteins with no match to a database entry. The entire genome is expected to comprise some 13000 protein coding genes, more than twice as many as found in yeasts, and reflects the high potential of filamentous fungi to cope with various environmental conditions.