Septin-Associated Protein Kinases in the Yeast Saccharomyces cerevisiae

Decoding post-translational modifications of mammalian septins

Septins are cytoskeletal GTPases that form nonpolar filaments and higher-ordered structures and they take part in a wide range of cellular processes. Septins are conserved from yeast to mammals but absent from higher plants. The number of septin genes vary between organisms and they usually form complex heteropolymeric networks. Most septins are known to be capable of GTP hydrolysis which may regulate septin dynamics. Knowledge on regulation of septin function by post-translational modifications is still in its infancy. In this review article, we highlight the post-translational modifications reported for the 13 human septins and discuss their implications on septin functions. In addition to the functionally investigated modifications, we also try to make sense of the complex septin post-translational modification code revealed from large-scale phospho-proteomic datasets. Future studies may determine how these isoform-specific and homology group specific modifications affect septin structure and function.

Phosphoregulation of the septin cytoskeleton in neuronal development and disease

Septins are highly conserved GTP-binding proteins that oligomerize and form higher order structures. The septin cytoskeleton plays an important role in cellular organization, intracellular transport, and cytokinesis. Kinase-mediated phosphorylation of septins regulates various aspects of their function, localization, and dynamics. Septins are enriched in the mammalian nervous system where they contribute to neurodevelopment and neuronal function. Emerging research has implicated aberrant changes in septin cytoskeleton in several human diseases. The mechanisms through which aberrant phosphorylation by kinases contributes to septin dysfunction in neurological disorders are poorly understood and represent an important question for future research with therapeutic implications. This review summarizes the current state of knowledge of the diversity of kinases that interact with and phosphorylate mammalian septins, delineates how phosphoregulation impacts septin dynamics, and describes how aberrant septin phosphorylation contributes to neurological disorders.

The Mitogen-Activated Protein Kinase Slt2 Promotes Asymmetric Cell Cycle Arrest and Reduces TORC1-Sch9 Signaling in Yeast Lacking the Protein Phosphatase Ptc1

Mitogen-activated protein kinase (MAPK) pathways regulate essential processes in eukaryotes. However, since uncontrolled activation of these cascades has deleterious effects, precise negative regulation of signaling flow through them, mainly executed by protein phosphatases, is crucial. Previous studies showed that the absence of Ptc1 protein phosphatase results in the upregulation of the MAPK of the cell wall integrity (CWI) pathway, Slt2, and numerous functional defects in Saccharomyces cerevisiae, including a failure to undergo cell separation under heat stress. In this study, we demonstrate that multibudded ptc1Δ cells also exhibit impaired mitochondrial inheritance and that excessive Slt2 kinase activity is responsible for their growth deficiency and daughter-specific G1 cell cycle arrest, as well as other physiological alterations, namely, mitochondrial hyperpolarization and reactive oxygen species (ROS) accumulation. We bring to light the fact that sustained Slt2 kinase activity inhibits signaling through the Sch9 branch of the TORC1 pathway in ptc1Δ cells, leading to increased autophagy. After cytokinesis, septin rings asymmetrically disassembled in ptc1Δ multibudded cells, abnormally remaining at the daughter cell side and eventually relocalizing at the daughter cell periphery, where they occasionally colocalized with the autophagic protein Atg9. Finally, we show that the inability of ptc1Δ cells to undergo cell separation is not due to a failure in the regulation of Ace2 and morphogenesis (RAM) pathway, since the transcription factor Ace2 correctly enters the daughter cell nuclei. However, the Ace2-regulated endochitinase Cts1 did not localize to the septum, preventing the proper degradation of this structure. IMPORTANCE This study provides further evidence that the cell cycle is regulated by complex signaling networks whose purpose is to guarantee a robust response to environmental threats. Using the S. cerevisiae eukaryotic model, we show that, under the stress conditions that activate the CWI MAPK pathway, the absence of the protein phosphatase Ptc1 renders Slt2 hyperactive, leading to numerous physiological alterations, including perturbed mitochondrial inheritance, oxidative stress, changes in septin dynamics, increased autophagy, TORC1-Sch9 inhibition, and ultimately cell cycle arrest and the failure of daughter cells to separate, likely due to the absence of key degradative enzymes at the septum. These results imply novel roles for the CWI pathway and unravel new cell cycle-regulatory controls that operate beyond the RAM pathway, arresting buds in G1 without compromising further division rounds in the mother cell.

Novel evolved Yarrowia lipolytica strains for enhanced growth and lipid content under high concentrations of crude glycerol

BACKGROUND

Yarrowia lipolytica is a well-studied oleaginous yeast known for its ability to accumulate and store intracellular lipids, while growing on diverse, non-conventional substrates. Amongst them, crude glycerol, a low-cost by-product of the biodiesel industry, appears to be an interesting option for scaling up a sustainable single-cell oil production process. Adaptive laboratory evolution (ALE) is a powerful tool to force metabolic adaptations endowing tolerance to stressful environmental conditions, generating superior phenotypes with industrial relevance.

RESULTS

Y. lipolytica MUCL 28849 underwent ALE in a synthetic medium with increasing concentration of pure or crude glycerol as a stressing factor (9-20% v/v) for 520 generations. In one case of pure glycerol, chemical mutagenesis with ethyl methanesulfonate (EMS) was applied prior to ALE. Growth profile, biomass production and lipid content of 660 evolved strains (EVS), revealed 5 superior isolates; exhibiting from 1.9 to 3.6-fold increase of dry biomass and from 1.1 to 1.6-fold increase of lipid concentration compared to the parental strain, when grown in 15% v/v crude glycerol. NGS for differential gene expression analysis, showed induced expression in all EVS affecting nucleosomal structure and regulation of transcription. As strains differentiated, further changes accumulated in membrane transport and protein transport processes. Genes involved in glycerol catabolism and triacylglycerol biosynthesis were overexpressed in two EVS. Mismatches and gaps in the expressed sequences identified altered splicing and mutations in the EVS, with most of them, affecting different components of septin ring formation in the budding process. The selected YLE155 EVS, used for scale-up cultivation in a 3L benchtop bioreactor with 20% v/v crude glycerol, achieved extended exponential phase, twofold increase of dry biomass and lipid yields at 48 h, while citric acid secretion and glycerol consumption rates were 40% and 50% lower, respectively, compared to the parental strain, after 24 h of cultivation.

CONCLUSION

ALE and EMS-ALE under increasing concentrations of pure or crude glycerol generated novel Y. lipolytica strains with enhanced biomass and lipid content. Differential gene expression analysis and scale-up of YLE155, illustrated the potential of the evolved strains to serve as suitable "chassis" for rational engineering approaches towards both increased lipid accumulation, and production of high-added value compounds, through efficient utilization of crude glycerol.

Effects of Septin-14 Gene Deletion on Adult Cognitive/Emotional Behavior

While various septin GTPases have been reported for their physiological functions, their roles in orchestrating complex cognitive/emotional functions in adult mammals remained scarcely explored. A comprehensive behavioral test battery was administered to two sexes of 12-week-old Septin-14 (SEPT14) knockout (KO) and wild-type (WT) mice. The sexually dimorphic effects of brain SEPT14 KO on inhibitory avoidance (IA) and hippocampal mGluR5 expression were noticed with greater IA latency and elevated mGluR5 level exclusively in male KO mice. Moreover, SEPT14 KO appeared to be associated with stress-provoked anxiety increase in a stress-related navigation task regardless of animals’ sexes. While male and female WT mice demonstrated comparable cell proliferation in the dorsal and ventral hippocampal dentate gyrus (DG), both sexes of SEPT14 KO mice had increased cell proliferation in the ventral DG. Finally, male and female SEPT14 KO mice displayed dampened observational fear conditioning magnitude and learning-provoked corticosterone secretion as compared to their same-sex WT mice. These results, taken together, prompt us to conclude that male, but not female, mice lacking the Septin-14 gene may exhibit increased aversive emotion-related learning and dorsal/ventral hippocampal mGluR5 expressions. Moreover, deletion of SEPT14 may be associated with elevated ventral hippocampal DG cell proliferation and stress-provoked anxiety-like behavior, while dampening vicarious fear conditioning magnitudes.

Characterization of Bud3 domains sufficient for bud neck targeting in S. cerevisiae

The cytoskeleton serves a diverse set of functions in both multi- and unicellular organisms, including movement, transport, morphology, cell division and cell signalling. The septin family of cytoskeletal proteins are found within all fungi and metazoans and can generate three-dimensional scaffolds in vivo that promote membrane curvature, serve as physical barriers and coordinate cell cycle checkpoints. In budding yeast, the septins organize into polymerized filaments that decorate the division site between mother and daughter cells during mitosis; assembly of this structure at the ‘bud neck’ is critical for completion of cytokinesis and execution of numerous other cellular events. One such pathway includes bud site selection and the recruitment of proteins such as Bud4 and Bud3 that are responsible for promoting an axial budding pattern in haploid yeast. While Bud4 appears to be recruited to the septins independently of the presence of Bud3, it is likely that Bud3 can localize to the bud neck using both Bud4-dependent and Bud4-independent mechanisms. Furthermore, it remains unclear which precise domain or domains within Bud3 is/are both necessary and sufficient for optimal association at the septin structure. In this study, we examined the localization of GFP-Bud3 constructs in otherwise wild-type (WT) haploid yeast cells expressing Cdc10-mCherry using fluorescence microscopy; we tested a collection of N- and C-terminal truncations and fusions of separate Bud3 protein elements to identify the smallest domain(s) responsible for bud neck localization. We found that the coordinate action of the central amphipathic helix (residues 847–865) and a partially conserved C-terminal motif (residues 1172–1273) was sufficient to promote bud neck recruitment in the presence of endogenous Bud3. This domain is considerably smaller than the previously characterized C-terminal portion required to physically interact with Bud4 (1221–1636) and utilizes a similar mechanism of pairing membrane association, with a separate localization domain, similar to other non-septin proteins targeted to the division site during cell division.

Septin Assembly and Remodeling at the Cell Division Site During the Cell Cycle

The septin family of proteins can assemble into filaments that further organize into different higher order structures to perform a variety of different functions in different cell types and organisms. In the budding yeast Saccharomyces cerevisiae, the septins localize to the presumptive bud site as a cortical ring prior to bud emergence, expand into an hourglass at the bud neck (cell division site) during bud growth, and finally “split” into a double ring sandwiching the cell division machinery during cytokinesis. While much work has been done to understand the functions and molecular makeups of these structures, the mechanisms underlying the transitions from one structure to another have largely remained elusive. Recent studies involving advanced imaging and in vitro reconstitution have begun to reveal the vast complexity involved in the regulation of these structural transitions, which defines the focus of discussion in this mini-review.

Reconstructed evolutionary history of the yeast septins Cdc11 and Shs1

Septins are GTP-binding proteins conserved across metazoans. They can polymerize into extended filaments and, hence, are considered a component of the cytoskeleton. The number of individual septins varies across the tree of life—yeast (Saccharomyces cerevisiae) has seven distinct subunits, a nematode (Caenorhabditis elegans) has two, and humans have 13. However, the overall geometric unit (an apolar hetero-octameric protomer and filaments assembled there from) has been conserved. To understand septin evolutionary variation, we focused on a related pair of yeast subunits (Cdc11 and Shs1) that appear to have arisen from gene duplication within the fungal clade. Either Cdc11 or Shs1 occupies the terminal position within a hetero-octamer, yet Cdc11 is essential for septin function and cell viability, whereas Shs1 is not. To discern the molecular basis of this divergence, we utilized ancestral gene reconstruction to predict, synthesize, and experimentally examine the most recent common ancestor (“Anc.11-S”) of Cdc11 and Shs1. Anc.11-S was able to occupy the terminal position within an octamer, just like the modern subunits. Although Anc.11-S supplied many of the known functions of Cdc11, it was unable to replace the distinct function(s) of Shs1. To further evaluate the history of Shs1, additional intermediates along a proposed trajectory from Anc.11-S to yeast Shs1 were generated and tested. We demonstrate that multiple events contributed to the current properties of Shs1: (1) loss of Shs1–Shs1 self-association early after duplication, (2) co-evolution of heterotypic Cdc11–Shs1 interaction between neighboring hetero-octamers, and (3) eventual repurposing and acquisition of novel function(s) for its C-terminal extension domain. Thus, a pair of duplicated proteins, despite constraints imposed by assembly into a highly conserved multi-subunit structure, could evolve new functionality via a complex evolutionary pathway.

The LKB1-like Kinase Elm1 Controls Septin Hourglass Assembly and Stability by Regulating Filament Pairing

Septins form rod-shaped hetero-oligomeric complexes that assemble into filaments and other higher-order structures, such as rings or hourglasses, at the cell division site in fungal and animal cells [1-4] to carry out a wide range of functions, including cytokinesis and cell morphogenesis. However, the architecture of septin higher-order assemblies and their control mechanisms, including regulation by conserved kinases [5, 6], remain largely unknown. In the budding yeast Saccharomyces cerevisiae, the five mitotic septins (Cdc3, Cdc10, Cdc11, Cdc12, and Shs1) localize to the bud neck and form an hourglass before cytokinesis that acts as a scaffold for proteins involved in multiple processes as well as a membrane-diffusible barrier between the mother and developing bud [7-9]. The hourglass is remodeled into a double ring that sandwiches the actomyosin ring at the onset of cytokinesis [10-13]. How septins are assembled into a highly ordered hourglass structure at the division site [13] is largely unexplored. Here we show that the LKB1-like kinase Elm1, which has been implicated in septin organization [14], cell morphogenesis [15], and mitotic exit [16, 17], specifically associates with the septin hourglass during the cell cycle and controls hourglass assembly and stability, especially for the daughter half, by regulating filament pairing and the functionality of its substrate, the septin-binding protein Bni5. This study illustrates how a protein kinase regulates septin architecture at the filament level and suggests that filament pairing is a highly regulated process during septin assembly and remodeling in vivo.

A blueprint of septin expression in human tissues

Septins are GTP-binding proteins that polymerize to form filaments involved in several important biological processes. In human, 13 distinct septins genes are classified in four groups. Filaments formed by septins are complex and usually involve members of each group in specific positions. Expression data from GTEx database, a publicly available expression database with thousands of samples derived from multiple human tissues, was used to evaluate the expression of septins. The brain is noticeably a hotspot for septin expression where few genes contribute to a large portion of septin transcript pool. Co-expression data between septins suggests two predominant specific complexes in brain tissues and one filament in other tissues. SEPT3 and SEPT5 are two genes highly expressed in the brain and with a strong co-expression in all brain tissues. Additional analysis shows that the expression of these two genes is highly variable between individuals, but significantly dependent on the individual's age. Age-dependent decrease of expression from those two septins involved in synapses reinforces their possible link with cognitive decay and neurodegenerative diseases associated with aging. Analysis of enrichment of Gene Ontology terms from lists of genes consistently co-expressed with septins suggests participation in diverse biological processes, pointing out some novel roles for septins. Interestingly, we observed strong consistency of some of these terms with experimentally described roles of septins. Coordination of septins expression with genes involved in DNA repair and cell cycle control may provide insights for previously described links between septins and cancer.

Septin-associated proteins Aim44 and Nis1 traffic between the bud neck and the nucleus in the yeast Saccharomyces cerevisiae

In budding yeast, a collar of septin filaments at the neck between a mother cell and its bud marks the incipient site for cell division and serves as a scaffold that recruits proteins required for proper spatial and temporal execution of cytokinesis. A set of interacting proteins that localize at or near the bud neck, including Aim44/Gps1, Nba1 and Nis1, also has been implicated in preventing Cdc42-dependent bud site re-establishment at the division site. We found that, at their endogenous level, Aim44 and Nis1 robustly localize sequentially at the septin collar. Strikingly, however, when overproduced, both proteins shift their subcellular distribution predominantly to the nucleus. Aim44 localizes with the inner nuclear envelope, as well as at the plasma membrane, whereas Nis1 accumulates within the nucleus, indicating that these proteins normally undergo nucleocytoplasmic shuttling. Of the 14 yeast karyopherins, Kap123/Yrb4 is the primary importin for Aim44, whereas several importins mediate Nis1 nuclear entry. Conversely, Kap124/Xpo1/Crm1 is the primary exportin for Nis1, whereas both Xpo1 and Cse1/Kap109 likely contribute to Aim44 nuclear export. Even when endogenously expressed, Nis1 accumulates in the nucleus when Nba1 is absent. When either Aim44 or Nis1 are overexpressed, Nba1 is displaced from the bud neck, further consistent with the mutual interactions of these proteins. Collectively, our results indicate that a previously unappreciated level at which localization of septin-associated proteins is controlled is via regulation of their nucleocytoplasmic shuttling, which places constraints on their availability for complex formation with other partners at the bud neck.