Comparative proteomics of mitosis and meiosis in Saccharomyces cerevisiae

Evidence of 14-3-3 proteins contributing to kinetochore integrity and chromosome congression during mitosis

The 14-3-3 family of proteins are conserved across eukaryotes and serve myriad important regulatory functions in the cell. Homo- and hetero-dimers of these proteins mainly recognize their ligands via conserved motifs to modulate the localization and functions of those effector ligands. In most of the genetic backgrounds of Saccharomyces cerevisiae, disruption of both 14-3-3 homologs (Bmh1 and Bmh2) are either lethal or cells survive with severe growth defects, including gross chromosomal missegregation and prolonged cell cycle arrest. To elucidate their contributions to chromosome segregation, in this work, we investigated their centromere- and kinetochore-related functions of Bmh1 and Bmh2. Analysis of appropriate deletion mutants shows that Bmh isoforms have cumulative and non-shared isoform-specific contributions in maintaining the proper integrity of the kinetochore ensemble. Consequently, Bmh mutant cells exhibited perturbations in kinetochore-microtubule (KT-MT) dynamics, characterized by kinetochore declustering, mis-localization of kinetochore proteins and Mad2-mediated transient G2/M arrest. These defects also caused an asynchronous chromosome congression in bmh mutants during metaphase. In summary, this report advances the knowledge on contributions of budding yeast 14-3-3 proteins in chromosome segregation by demonstrating their roles in kinetochore integrity and chromosome congression.

Lyophilized yeast powder for adjuvant free thermostable vaccine delivery

Thermolabile nature of commercially available vaccines necessitates their storage, transportation, and dissemination under refrigerated condition. Maintenance of continuous cold chain at every step increases the final cost of vaccines. Any breach in the cold chain even for a short duration results in the need to discard the vaccines. As a result, there is a pressing need for the development of thermostable vaccines. In this proof-of-concept study, we showed that E. coli curli-green fluorescent fusion protein remains stable in freeze-dried yeast powder for more than 18 and 12 months when stored at 30 °C and 37 °C respectively. Stability of the heterologous protein remains unaffected during the process of heat-inactivation and lyophilization. The mass of lyophilized yeast powder remains almost unchanged during the entire period of storage and expressed protein remains intact even after two cycles of freeze and thaws. The protease-deficient strain appears ideal for the development of whole recombinant yeast-based vaccines. The cellular abundance of expressed antigen in dry powder after a year was comparable to freshly lyophilized cells. Scanning electron microscopy showed the intact nature of cells in powdered form even after a year of storage at 30 °C. Observation made in this study showed that freeze-dry yeast powder can play a vital role in the development of thermostable vaccines.

Key Points

• Yeast-based vaccines can overcome problem of cold chain associated with conventional vaccines

• Lyophilized yeast powder can be a simple way for long-term storage of immunogen(s)

• Protease deficient strain is important for whole recombinant yeast-based vaccines

Investigating the long-term stability of protein immunogen(s) for whole recombinant yeast-based vaccines

Even today vaccine(s) remains a mainstay in combating infectious diseases. Many yeast-based vaccines are currently in different phases of clinical trials. Despite the encouraging results of whole recombinant yeast and yeast display, the systematic study assessing the long-term stability of protein antigen(s) in yeast cells is still missing. Therefore, in the present study, I investigate the stability of heterologous protein antigen in the cellular environment of Saccharomyces cerevisiae through Escherichia coli surface protein (major curlin or CsgA). Present biochemical data showed that the stationary-phase yeast cells were able to keep the antigen stable for almost 1 year when stored at 2°C-8°C and 23°C-25°C. Further, iTRAQ-based quantitative proteomics of yeast whole cell lysate showed that the level of heterologous fusion protein was low in cells stored at 23°C-25°C compared to those at 2°C-8°C. In the end, I also proposed a workable strategy to test the integrity or completeness of heterologous protein in the yeast cell. I believe that the observations made in the present study will be really encouraging for those interested in the development of a whole recombinant yeast-based vaccine(s).

Simplified protocol for faster transformation of (a large number of) Pichia pastoris strains

During the last couple of decades, the methylotrophic yeast, Pichia pastoris, has emerged as an important yeast species owing to its increasing importance both in industry and in basic research. The presently available methods for P. pastoris transformation necessitate the preparation of competent cells, which requires lots of resource, space, time, and efforts. This limits the number of transformations that can be performed by an individual in a given time. This paper is reporting a modification in the available protocols, which makes P. pastoris transformation hassle-free. In the present, modified procedure, cells were grown in patches on YPD plate(s), and the rest of the steps were carried out in small Eppendorf tubes. This modified protocol does not require a big centrifuge and shaker. This modified procedure of P. pastoris transformation with its unique way of competent cells preparation will be helpful for those working with this yeast species.

Applying the auxin-inducible degradation system for rapid protein depletion in mammalian cells

The ability to deplete a protein of interest is critical for dissecting cellular processes. Traditional methods of protein depletion are often slow acting, which can be problematic when characterizing a cellular process that occurs within a short period of time, such as mitosis. Furthermore, these methods are usually not reversible. Recent advances to achieve protein depletion function by inducibly trafficking proteins of interest to an endogenous E3 ubiquitin ligase complex to promote ubiquitination and subsequent degradation by the proteasome. One of these systems, the auxin-inducible degron (AID) system, has been shown to permit rapid and inducible degradation of AID-tagged target proteins in mammalian cells. The AID system can control the abundance of a diverse set of cellular proteins, including those contained within protein complexes, and is active in all phases of the cell cycle. Here we discuss considerations for the successful implementation of the AID system and describe a protocol using CRISPR/Cas9 to achieve biallelic insertion of an AID in human cells. This method can also be adapted to insert other tags, such as fluorescent proteins, at defined genomic locations.

Differential abundance and transcription of 14-3-3 proteins during vegetative growth and sexual reproduction in budding yeast

14-3-3 is a family of relatively low molecular weight, acidic, dimeric proteins, conserved from yeast to metazoans including humans. Apart from their role in diverse cellular processes, these proteins are also known for their role in several clinical implications. Present proteomic and biochemical comparison showed increased abundance and differential phosphorylation of these proteins in meiotic cells. Double deletion of bmh1^−/−bmh2^−/− leads to complete absence of sporulation with cells arrested at G₁/S phase while further incubation of cells in sporulating media leads to cell death. In silico analysis showed the presence of 14-3-3 interacting motifs in bonafide members of kinetochore complex (KC) and spindle pole body (SPB), while present cell biological data pointed towards the possible role of yeast Bmh1/2 in regulating the behaviour of KC and SPB. We further showed the involvement of 14-3-3 in segregation of genetic material and expression of human 14-3-3β/α was able to complement the function of endogenous 14-3-3 protein even in the complex cellular process like meiosis. Our present data also established haplosufficient nature of BMH1/2. We further showed that proteins synthesized during mitotic growth enter meiotic cells without de novo synthesis except for meiotic-specific proteins required for induction and meiotic progression in Saccharomyces cerevisiae.

An account of fungal 14-3-3 proteins

14-3-3s are a group of relatively low molecular weight, acidic, dimeric, protein(s) conserved from single-celled yeast to multicellular vertebrates including humans. Despite lacking catalytic activity, these proteins have been shown to be involved in multiple cellular processes. Apart from their role in normal cellular physiology, recently these proteins have been implicated in various medical consequences. In this present review, fungal 14-3-3 protein localization, interactions, transcription, regulation, their role in the diverse cellular process including DNA duplication, cell cycle, protein trafficking or secretion, apoptosis, autophagy, cell viability under stress, gene expression, spindle positioning, role in carbon metabolism have been discussed. In the end, I also highlighted various roles of yeasts 14-3-3 proteins in tabular form. Thus this review with primary emphasis on yeast will help in appreciating the significance of 14-3-3 proteins in cell physiology.

Quantitative proteomic comparison of stationary/G0 phase cells and tetrads in budding yeast

Most of the microbial cells on earth under natural conditions exist in a dormant condition, commonly known as quiescent state. Quiescent cells exhibit low rates of transcription and translation suggesting that cellular abundance of proteins may be similar in quiescent cells. Therefore, this study aim to compare the proteome of budding yeast cells from two quiescent states viz. stationary phase/G0 and tetrads. Using iTRAQ (isobaric tag for relative and absolute quantitation) based quantitative proteomics we identified 289 proteins, among which around 40 proteins exhibited ±1.5 fold change consistently from the four biological replicates. Proteomics data was validated by western blot and denstiometric analysis of Hsp12 and Spg4. Level of budding yeast 14-3-3 proteins was found to be similar in both the quiescent states, whereas Hsp12 and Spg4 expressed only during stress. FACS (fluorescence-activated cell sorting) analysis showed that budding yeast cells were arrested at G1 stages both in tetrads as well as in stationary phase. We also observed that quiescent states did not express Ime1 (inducer of meiosis). Taken together, our present study demonstrates that the cells in quiescent state may have similar proteome, and accumulation of proteins like Hsp12, Hsp26, and Spg4 may play an important role in retaining viability of the cells during dormancy.

Similar environments but diverse fates: Responses of budding yeast to nutrient deprivation

Diploid budding yeast (Saccharomyces cerevisiae) can adopt one of several alternative differentiation fates in response to nutrient limitation, and each of these fates provides distinct biological functions. When different strain backgrounds are taken into account, these various fates occur in response to similar environmental cues, are regulated by the same signal transduction pathways, and share many of the same master regulators. I propose that the relationships between fate choice, environmental cues and signaling pathways are not Boolean, but involve graded levels of signals, pathway activation and master-regulator activity. In the absence of large differences between environmental cues, small differences in the concentration of cues may be reinforced by cell-to-cell signals. These signals are particularly essential for fate determination within communities, such as colonies and biofilms, where fate choice varies dramatically from one region of the community to another. The lack of Boolean relationships between cues, signaling pathways, master regulators and cell fates may allow yeast communities to respond appropriately to the wide range of environments they encounter in nature.