Structural analysis of <Emphasis Type="Italic">N</Emphasis>-/<Emphasis Type="Italic">O</Emphasis>-glycans assembled on proteins in yeasts

Protein glycosylation, the most universal and diverse post-translational modification, can affect protein secretion, stability, and immunogenicity. The structures of glycans attached to proteins are quite diverse among different organisms and even within yeast species. In yeast, protein glycosylation plays key roles in the quality control of secretory proteins, and particularly in maintaining cell wall integrity. Moreover, in pathogenic yeasts, glycans assembled on cell-surface glycoproteins can mediate their interactions with host cells. Thus, a comprehensive understanding of protein glycosylation in various yeast species and defining glycan structure characteristics can provide useful information for their biotechnological and clinical implications. Yeast-specific glycans are a target for glyco-engineering; implementing human-type glycosylation pathways in yeast can aid the production of recombinant glycoproteins with therapeutic potential. The virulenceassociated glycans of pathogenic yeasts could be exploited as novel targets for antifungal agents. Nowadays, several glycomics techniques facilitate the generation of species-and strain-specific glycome profiles and the delineation of modified glycan structures in mutant and engineered yeast cells. Here, we present the protocols employed in our laboratory to investigate the N-and O-glycan chains released from purified glycoproteins or cell wall mannoproteins in several yeast species.     

Glycosylation control technologies for recombinant therapeutic proteins

Protein glycosylation is a very important quality attribute of any biopharmaceutical product as it affects the efficacy, serum half-life, and antigenicity of a molecule. The present expression hosts commercially utilized for a recombinant glycoprotein production generally cannot produce a desired and uniform glycan composition and generally exhibit non-human glycans that can lead to unwanted side effects. The authors provide a comprehensive review of various approaches which can be implemented to minimize the glycan heterogeneity for the production of the desired protein with improved glycoforms. The authors also describe that the industry standard expression systems such as mammalian, insect, and yeast are glycoengineered to produce human-like glycan composition of a recombinant product. This review summarizes the recent technologies used for the improvement of the glycan composition of the biotherapeutics, focusing largely on the selection of an appropriate expression host, glycoengineering, and upstream process optimization to control protein glycosylation and thus enhanced biological activity with fewer side effects. Here, we also suggest various approaches such as host and clone selection to achieve expected glycosylation in a recombinant protein. The cell culture, biochemical, and physical process parameters play a key role in the manufacturing of the desired glycoform of a therapeutic protein. Hence, these components are to be considered very carefully while developing such glycoproteins. Also, glycoengineering of production host to modulate the protein glycosylation is also recommended in the present review.

     

Hydrocortisone made in yeast: metabolic engineering turns a unicellular microorganism into a drug-synthesizing factory

Inspired by the successful work of converting Saccharomyces cerevisiae into an microorganism capable of synthesizing hydrocortisone, a 27-carbon molecule, from ethanol, a 2-carbon molecule, this review provides an overview of the potential of yeast as a recombinant organism in the 21st century. Yeast has been used by man for more than 6,000 years, and is still paving the way to new discoveries. It was the first eukaryotic organism to be sequenced, in 1996, and the first to produce hydrocortisone in 2003. In addition, extensive genome-wide analyses have been performed with yeast. In this review, we discuss the pros and cons of using yeast to produce small therapeutic molecules. It is obvious that S. cerevisiae has a cutting edge advantage of being a well-known organism and time will tell if yeast "biohydrocortisone" is a unique example or the beginning of a long list of yeast bioproducts. Other organisms, such as plants and bacteria, are competing with yeast. Bacteria produce a wealth of marketed molecules and plants are capable of producing extremely complex molecules with an unbeatable yield. However, S. cerevisiae offers a unique mix of the simplicity of a recombinant organism combined with the complexity of a eukaryote.     

What is the total number of protein molecules per cell volume? A call to rethink some published values

Novel methods such as mass‐spectrometry enable a view of the proteomes of cells in unprecedented detail. Recently, these efforts have culminated in quantitative measurements of the number of copies per cell for most expressed proteins in organisms ranging from bacteria to mammalian cells. Here, we estimate the expected total number of proteins per unit of cell volume using known parameters related to the composition of cells such as the fraction of cell mass that is protein, and the average protein length. Using simple arguments, we estimate a range of 2–4 million proteins per cubic micron (i.e. 1 fL) in bacteria, yeast, and mammalian cells. Interestingly, we find that measured values that are reported for fission yeast and mammalian cells are often about 3–10 times lower. We discuss this apparent discrepancy and how to use the estimate as benchmark to recalibrate proteome‐wide quantitative censuses or to revisit assumptions about cell composition.     

An engineered Saccharomyces cerevisiae strain binds the broadly neutralizing human immunodeficiency virus type 1 antibody 2G12 and elicits mannose-specific gp120-binding antibodies

The glycan shield of the human immunodeficiency virus type 1 (HIV-1) envelope (Env) protein serves as a barrier to antibody-mediated neutralization and plays a critical role in transmission and infection. One of the few broadly neutralizing HIV-1 antibodies, 2G12, binds to a carbohydrate epitope consisting of an array of high-mannose glycans exposed on the surface of the gp120 subunit of the Env protein. To produce proteins with exclusively high-mannose carbohydrates, we generated a mutant strain of Saccharomyces cerevisiae by deleting three genes in the N-glycosylation pathway, Och1, Mnn1, and Mnn4. Glycan profiling revealed that N-glycans produced by this mutant were almost exclusively Man(8)GlcNAc(2), and four endogenous glycoproteins that were efficiently recognized by the 2G12 antibody were identified. These yeast proteins, like HIV-1 gp120, contain a large number and high density of N-linked glycans, with glycosidase digestion abrogating 2G12 cross-reactivity. Immunization of rabbits with whole Delta och1 Delta mnn1 Delta mnn4 yeast cells produced sera that recognized a broad range of HIV-1 and simian immunodeficiency virus (SIV) Env glycoproteins, despite no HIV/SIV-related proteins being used in the immunization procedure. Analyses of one of these sera on a glycan array showed strong binding to glycans with terminal Man alpha1,2Man residues, and binding to gp120 was abrogated by glycosidase removal of high-mannose glycans and terminal Man alpha1,2Man residues, similar to 2G12. Since S. cerevisiae is genetically pliable and can be grown easily and inexpensively, it will be possible to produce new immunogens that recapitulate the 2G12 epitope and may make the glycan shield of HIV Env a practical target for vaccine development.     

Biogenesis of lipid droplets--how cells get fatter

Lipid droplets are discrete organelles present in most cell types and organisms including bacteria, yeast, plants, insects and animals. Long considered as passive storage deposits, recent cell biology, proteomic and lipidomic analysis show that lipid droplets are dynamic organelles involved in multiple cellular functions. They have a central function in lipid distribution to different membrane-bound organelles and serve not only as main reservoirs of neutral lipids such as triglycerides and cholesterol but in addition, contain structural proteins, proteins involved in lipid synthesis and transmembrane proteins. A detailed model for how transmembrane proteins such as SNARE proteins can exist in lipid droplets is proposed.     

Biogenesis of lipid droplets – how cells get fatter

Abstract

Lipid droplets are discrete organelles present in most cell types and organisms including bacteria, yeast, plants, insects and animals. Long considered as passive storage deposits, recent cell biology, proteomic and lipidomic analysis show that lipid droplets are dynamic organelles involved in multiple cellular functions. They have a central function in lipid distribution to different membrane-bound organelles and serve not only as main reservoirs of neutral lipids such as triglycerides and cholesterol but in addition, contain structural proteins, proteins involved in lipid synthesis and transmembrane proteins. A detailed model for how transmembrane proteins such as SNARE proteins can exist in lipid droplets is proposed.     

Insects, oxygen, and iron

Konrad Bloch developed an interest in insects because they are unable to make sterols, and in yeast because these cells need oxygen to make sterols and unsaturated fatty acids. Insects, like all other organisms, must deal with the toxic effects of oxygen in the presence of iron, which itself is a vital nutrient. They do so by making proteins with high affinity for ferric or ferrous ions. Two such proteins are transferrins and ferritins. Insects produce both of these proteins, but use them in different ways from most other organisms. Insect transferrins appear to be involved in innate immunity, perhaps by sequestering ferric ions to prevent pathogens and parasites from utilizing them. Insect ferritins, unlike those of any other group of organisms, are exported into the extracellular space (hemolymph). They may be involved in iron transport and/or protection against iron overload in the diet.     

The expanding horizons of asparagine-linked glycosylation

Asparagine-linked glycosylation involves the sequential assembly of an oligosaccharide onto a polyisoprenyl donor, followed by the en bloc transfer of the glycan to particular asparagine residues within acceptor proteins. These N-linked glycans play a critical role in a wide variety of biological processes, such as protein folding, cellular targeting and motility, and the immune response. In the past decade, research in the field of N-linked glycosylation has achieved major advances, including the discovery of new carbohydrate modifications, the biochemical characterization of the enzymes involved in glycan assembly, and the determination of the biological impact of these glycans on target proteins. It is now firmly established that this enzyme-catalyzed modification occurs in all three domains of life. However, despite similarities in the overall logic of N-linked glycoprotein biosynthesis among the three kingdoms, the structures of the appended glycans are markedly different and thus influence the functions of elaborated proteins in various ways. Though nearly all eukaryotes produce the same nascent tetradecasaccharide (Glc(3)Man(9)GlcNAc(2)), heterogeneity is introduced into this glycan structure after it is transferred to the protein through a complex series of glycosyl trimming and addition steps. In contrast, bacteria and archaea display diversity within their N-linked glycan structures through the use of unique monosaccharide building blocks during the assembly process. In this review, recent progress toward gaining a deeper biochemical understanding of this modification across all three kingdoms will be summarized. In addition, a brief overview of the role of N-linked glycosylation in viruses will also be presented.     

Yeast glycobiology and its application

In this review, I describe the yeast glycans and their biosynthetic pathways, especially in the budding yeast Saccharomyces cerevisiae. The biosynthetic pathway of N-glycan in the endoplasmic reticulum is similar to that of mammalian cells, while the pathway in the Golgi is different from that of mammalian cells, but the biosynthetic pathway of O-glycan, mainly composed of O-oligomannoses, appears to be specific to yeast cells. Yeast systems are useful not only to understand the basic mechanisms of glycan synthesis but also to produce therapeutic proteins with human-type glycans. Protein modification by glycosylphosphatidylinositol is one of the major post-translational modifications in which oligosaccharides are involved. The biosynthetic pathway and the physiological function of glycosylphosphatidylinositol in S. cerevisiae are described in relation to lipid microdomains (also called "lipid rafts"), focusing on the latest findings related to lipid remodeling of GPI-anchored proteins.     

细菌血红素降解蛋白结构特点及作用机制

铁离子是几乎所有生物包括细菌生存必需的营养元素. 在宿主体内,绝大多数的铁离子均以血红素的形式存在于各种血红素结合蛋白,如血红蛋白、肌红蛋白等. 当致病菌感染宿主后,血红素将成为某些致病菌主要的铁离子来源. 致病菌编码血红素转运系统,并利用该系统将血红素转运至胞浆,在胞浆血红素被细菌的血红素降解蛋白降解,释放铁离子供细菌利用. 在致病菌中,目前至少有两种血红素降解酶被发现和鉴定. 第一种为经典的血红素氧化酶(heme oxygenase, HO),它催化血红素氧化形成胆绿素、一氧化碳(CO)和Fe2+;第二种非经典降解酶,包括金黄色葡萄球菌的IsdG/IsdI蛋白及其同系物MhuD蛋白,催化血红素分别产生staphylobilin和mycobilin. 另外,部分细菌内存在其它血红素降解因子,其与前两种血红素降解酶无结构同源性,但在血红素降解实验中可产生胆绿素(biliverdin)或CO,因而被鉴定为“血红素降解蛋白”. 对细菌血红素降解蛋白分子结构解析及作用机制的深入理解,将有助于新的血红素降解蛋白的发现和鉴定.     

Current methods for Saccharomyces cerevisiae. I. Growth

Interest in the study of yeast biology has increased dramatically in the past few years. Since these organisms are eukaryotic, some phenomena observed in yeast may provide a useful model for similar phenomena in multicellular organisms. Yeast has several advantages as an experimental organism and many methods used for bacteria can be adapted to them. Yeast is simple to grow, cultures are easily maintained, and classical and molecular genetic techniques can be used. The ability to approach problems genetically and biochemically has lead to substantive progess with this group of organisms in areas such as cell biology (1) and gene expression (2). This review is intended to introduce investigators to practical techniques for the growth and radioactive labeling of yeast, primarily of Saccharomyces cerevisiae. For genetic techniques, readers are referred to a recent laboratory manual (3) and reviews (4,5).     

Microorganism lipid droplets and biofuel development

Lipid droplet (LD) is a cellular organelle that stores neutral lipids as a source of energy and carbon. However, recent research has emerged that the organelle is involved in lipid synthesis, transportation, and metabolism, as well as mediating cellular protein storage and degradation. With the exception of multi-cellular organisms, some unicellular microorganisms have been observed to contain LDs. The organelle has been isolated and characterized from numerous organisms. Triacylglycerol (TAG) accumulation in LDs can be in excess of 50% of the dry weight in some microorganisms, and a maximum of 87% in some instances. These microorganisms include eukaryotes such as yeast and green algae as well as prokaryotes such as bacteria. Some organisms obtain carbon from CO2 via photosynthesis, while the majority utilizes carbon from various types of biomass. Therefore, high TAG content generated by utilizing waste or cheap biomass, coupled with an efficient conversion rate, present these organisms as bio-tech ‘factories’ to produce biodiesel. This review summarizes LD research in these organisms and provides useful information for further LD biological research and microorganism biodiesel development. [BMB Reports 2013; 46(12): 575-581]     

The ins and outs of bacterial iron metabolism

Iron is a critical nutrient for the growth and survival of most bacterial species. Accordingly, much attention has been paid to the mechanisms by which host organisms sequester iron from invading bacteria and how bacteria acquire iron from their environment. However, under oxidative stress conditions such as those encountered within phagocytic cells during the host immune response, iron is released from proteins and can act as a catalyst for Fenton chemistry to produce cytotoxic reactive oxygen species. The transitory efflux of free intracellular iron may be beneficial to bacteria under such conditions. The recent discovery of putative iron efflux transporters in Salmonella enterica serovar Typhimurium is discussed in the context of cellular iron homeostasis.     

Structural remodeling of GPI anchors during biosynthesis and after attachment to proteins

Glycosylphosphatidylinositol (GPI) anchoring of proteins is a conserved post-translational modification in eukaryotes. In mammalian cells, approximately 150 proteins on the plasma membrane are attached to the cell surface by GPI anchors, which confer specific properties on proteins, such as association with membrane microdomains. The structures of lipid and glycan moieties on GPI anchors are remodeled during biosynthesis and after attachment to proteins. The remodeling processes are critical for transport and microdomain-association of GPI-anchored proteins. Here, we describe the structural remodeling of GPI anchors and genes required for the processes in mammals, yeast, and trypanosomes.     

DNA mismatch repair system. Classical and fresh roles

The molecular mechanisms of the DNA mismatch repair (MMR) system have been uncovered over the last decade, especially in prokaryotes. The results obtained for prokaryotic MMR proteins have provided a framework for the study of the MMR system in eukaryotic organisms, such as yeast, mouse and human, because the functions of MMR proteins have been conserved during evolution from bacteria to humans. However, mutations in eukaryotic MMR genes result in pleiotropic phenotypes in addition to MMR defects, suggesting that eukaryotic MMR proteins have evolved to gain more diverse and specific roles in multicellular organisms. Here, we summarize recent advances in the understanding of both prokaryotic and eukaryotic MMR systems and describe various new functions of MMR proteins that have been intensively researched during the last few years, including DNA damage surveillance and diversification of antibodies.     

Interactions between the nitrogen signal transduction protein PII and N-acetyl glutamate kinase in organisms that perform oxygenic photosynthesis

PII, one of the most conserved signal transduction proteins, is believed to be a key player in the coordination of nitrogen assimilation and carbon metabolism in bacteria, archaea, and plants. However, the identity of PII receptors remains elusive, particularly in photosynthetic organisms. Here we used yeast two-hybrid approaches to identify new PII receptors and to explore the extent of conservation of PII signaling mechanisms between eubacteria and photosynthetic eukaryotes. Screening of Synechococcus sp. strain PCC 7942 libraries with PII as bait resulted in identification of N-acetyl glutamate kinase (NAGK), a key enzyme in the biosynthesis of arginine. The integrity of Ser49, a residue conserved in PII proteins from organisms that perform oxygenic photosynthesis, appears to be essential for NAGK binding. The effect of glnB mutations on NAGK activity is consistent with positive regulation of NAGK by PII. Phylogenetic and yeast two-hybrid analyses strongly suggest that there was conservation of the NAGK-PII regulatory interaction in the evolution of cyanobacteria and chloroplasts, providing insight into the function of eukaryotic PII-like proteins.     

Biosynthesis of glycosylphosphatidylinositols in mammals and unicellular microbes.

Membrane anchoring of cell surface proteins via glycosylphosphatidylinositol (GPI) occurs in all eukaryotic organisms. In addition, GPI-related glycophospholipids are important constituents of the glycan coat of certain protozoa. Defects in GPI biosynthesis can retard, if not abolish growth of these organisms. In humans, a defect in GPI biosynthesis can cause paroxysmal nocturnal hemoglobinuria (PNH), a severe acquired bone marrow disorder. Here, we review advances in the characterization of GPI biosynthesis in parasitic protozoa, yeast and mammalian cells. The GPI core structure as well as the major steps in its biosynthesis are conserved throughout evolution. However, there are significant biosynthetic differences between mammals and microbes. First indications are that these differences could be exploited as targets in the design of novel pharmacotherapeutics that selectively inhibit GPI biosynthesis in unicellular microbes.     

Protein glycosylation--an evolutionary crossroad between genes and environment

The majority of molecular processes in higher organisms are performed by various proteins and are thus determined by genes that encode these proteins. However, a significant structural component of at least half of all cellular proteins is not a polypeptide encoded by a single gene, but an oligosaccharide (glycan) synthesized by a network of proteins, resulting from the expression of hundreds of different genes. Relationships between hundreds of individual proteins that participate in glycan biosynthesis are very complex which enables the influence of environmental factors on the final structure of glycans, either by direct effects on individual enzymatic processes, or by induction of epigenetic changes that modify gene expression patterns. Until recently, the complexity of glycan structures prevented large scale studies of protein glycosylation, but recent advances in both glycan analysis and genotyping technologies, enabled the first insights into the intricate field of complex genetics of protein glycosylation. Mutations which inactivate genes involved in the synthesis of common N-glycan precursors are embryonically lethal. However, mutations in genes involved in modifications of glycan antennas are common and apparently contribute largely to individual phenotypic variations that exist in humans and other higher organisms. Some of these variations can be recognized as specific glyco-phenotypes that might represent specific evolutionary advantages or disadvantages. They are however, amenable to environmental influences and are thus less pre-determined than classical Mendelian mutations.