The fission yeast NIMA kinase Fin1p is required for spindle function and nuclear envelope integrity

Moonlighting at the Poles: Non-Canonical Functions of Centrosomes

Centrosomes are best known as the microtubule organizing centers (MTOCs) of eukaryotic cells. In addition to their classic role in chromosome segregation, centrosomes play diverse roles unrelated to their MTOC activity during cell proliferation and quiescence. Metazoan centrosomes and their functional doppelgängers from lower eukaryotes, the spindle pole bodies (SPBs), act as important structural platforms that orchestrate signaling events essential for cell cycle progression, cellular responses to DNA damage, sensory reception and cell homeostasis. Here, we provide a critical overview of the unconventional and often overlooked roles of centrosomes/SPBs in the life cycle of eukaryotic cells.

In Mitosis You Are Not: The NIMA Family of Kinases in Aspergillus, Yeast, and Mammals

The Never in mitosis gene A (NIMA) family of serine/threonine kinases is a diverse group of protein kinases implicated in a wide variety of cellular processes, including cilia regulation, microtubule dynamics, mitotic processes, cell growth, and DNA damage response. The founding member of this family was initially identified in Aspergillus and was found to play important roles in mitosis and cell division. The yeast family has one member each, Fin1p in fission yeast and Kin3p in budding yeast, also with functions in mitotic processes, but, overall, these are poorly studied kinases. The mammalian family, the main focus of this review, consists of 11 members named Nek1 to Nek11. With the exception of a few members, the functions of the mammalian Neks are poorly understood but appear to be quite diverse. Like the prototypical NIMA, many members appear to play important roles in mitosis and meiosis, but their functions in the cell go well beyond these well-established activities. In this review, we explore the roles of fungal and mammalian NIMA kinases and highlight the most recent findings in the field.

The Dictyostelium Centrosome

The centrosome of Dictyostelium amoebae contains no centrioles and consists of a cylindrical layered core structure surrounded by a corona harboring microtubule-nucleating γ-tubulin complexes. It is the major centrosomal model beyond animals and yeasts. Proteomics, protein interaction studies by BioID and superresolution microscopy methods led to considerable progress in our understanding of the composition, structure and function of this centrosome type. We discuss all currently known components of the Dictyostelium centrosome in comparison to other centrosomes of animals and yeasts.

Quantitative Phosphoproteomics Reveals the Signaling Dynamics of Cell-Cycle Kinases in the Fission Yeast Schizosaccharomyces pombe

Multiple protein kinases regulate cell-cycle progression, of which the cyclin-dependent kinases (CDKs) are thought to act as upstream master regulators. We have used quantitative phosphoproteomics to analyze the fission yeast cell cycle at sufficiently high temporal resolution to distinguish fine-grain differences in substrate phosphorylation dynamics on a proteome-wide scale. This dataset provides a useful resource for investigating the regulatory dynamics of cell-cycle kinases and their substrates. For example, our analysis indicates that the substrates of different mitotic kinases (CDK, NIMA-related, Polo-like, and Aurora) are phosphorylated in sequential, kinase-specific waves during mitosis. Phosphoproteomics analysis after chemical-genetic manipulation of CDK activity suggests that the timing of these waves is established by the differential dependency of the downstream kinases on upstream CDK. We have also examined the temporal organization of phosphorylation during G1/S, as well as the coordination between the NDR-related kinase Orb6, which controls polarized growth, and other cell-cycle kinases.

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Global analysis of phosphorylation dynamics during the fission yeast cell cycle

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Reveals kinase-specific waves of phosphorylation throughout interphase and mitosis

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Mitotic kinases show significantly different dependencies on upstream CDK activity

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Kinases directly downstream of CDK mediate earlier waves of mitotic phosphorylation

The NIMA kinase is required to execute stage-specific mitotic functions after initiation of mitosis

The G2-M transition in Aspergillus nidulans requires the NIMA kinase, the founding member of the Nek kinase family. Inactivation of NIMA results in a late G2 arrest, while overexpression of NIMA is sufficient to promote mitotic events independently of cell cycle phase. Endogenously tagged NIMA-GFP has dynamic mitotic localizations appearing first at the spindle pole body and then at nuclear pore complexes before transitioning to within nuclei and the mitotic spindle and back at the spindle pole bodies at mitotic exit, suggesting that it functions sequentially at these locations. Since NIMA is indispensable for mitotic entry, it has been difficult to determine the requirement of NIMA for subaspects of mitosis. We show here that when NIMA is partially inactivated, although mitosis can be initiated, a proportion of cells fail to successfully generate two daughter nuclei. We further define the mitotic defects to show that normal NIMA function is required for the formation of a bipolar spindle, nuclear pore complex disassembly, completion of chromatin segregation, and the normal structural rearrangements of the nuclear envelope required to generate two nuclei from one. In the remaining population of cells that enter mitosis with inadequate NIMA, two daughter nuclei are generated in a manner dependent on the spindle assembly checkpoint, indicating highly penetrant defects in mitotic progression without sufficient NIMA activity. This study shows that NIMA is required not only for mitotic entry but also sequentially for successful completion of stage-specific mitotic events.

Regulation of mitosis by the NIMA kinase involves TINA and its newly discovered partner, An-WDR8, at spindle pole bodies

The NIMA kinase is required for mitotic nuclear pore complex disassembly and potentially controls other mitotic-specific events. To investigate this possibility, we imaged NIMA-green fluorescent protein (GFP) using four-dimensional spinning disk confocal microscopy. At mitosis NIMA-GFP locates to spindle pole bodies (SPBs), which contain Cdk1/cyclin B, followed by Aurora, TINA, and the BimC kinesin. NIMA promotes NPC disassembly in a spatially regulated manner starting near SPBs. NIMA is also required for TINA, a NIMA-interacting protein, to locate to SPBs during initiation of mitosis, and TINA is then necessary for locating NIMA back to SPBs during mitotic progression. To help expand the NIMA-TINA pathway, we affinity purified TINA and found it to uniquely copurify with An-WDR8, a WD40-domain protein conserved from humans to plants. Like TINA, An-WDR8 accumulates within nuclei during G2 but disperses from nuclei before locating to mitotic SPBs. Without An-WDR8, TINA levels are greatly reduced, whereas TINA is necessary for mitotic targeting of An-WDR8. Finally, we show that TINA is required to anchor mitotic microtubules to SPBs and, in combination with An-WDR8, for successful mitosis. The findings provide new insights into SPB targeting and indicate that the mitotic microtubule-anchoring system at SPBs involves WDR8 in complex with TINA.

Cell cycle regulation by the NEK family of protein kinases

Genetic screens for cell division cycle mutants in the filamentous fungus Aspergillus nidulans led to the discovery of never-in-mitosis A (NIMA), a serine/threonine kinase that is required for mitotic entry. Since that discovery, NIMA-related kinases, or NEKs, have been identified in most eukaryotes, including humans where eleven genetically distinct proteins named NEK1 to NEK11 are expressed. Although there is no evidence that human NEKs are essential for mitotic entry, it is clear that several NEK family members have important roles in cell cycle control. In particular, NEK2, NEK6, NEK7 and NEK9 contribute to the establishment of the microtubule-based mitotic spindle, whereas NEK1, NEK10 and NEK11 have been implicated in the DNA damage response. Roles for NEKs in other aspects of mitotic progression, such as chromatin condensation, nuclear envelope breakdown, spindle assembly checkpoint signalling and cytokinesis have also been proposed. Interestingly, NEK1 and NEK8 also function within cilia, the microtubule-based structures that are nucleated from basal bodies. This has led to the current hypothesis that NEKs have evolved to coordinate microtubule-dependent processes in both dividing and non-dividing cells. Here, we review the functions of the human NEKs, with particular emphasis on those family members that are involved in cell cycle control, and consider their potential as therapeutic targets in cancer.

Remodeling the nuclear membrane during closed mitosis

The mitotic spindle assembly and chromosome segregation in eukaryotes must be coordinated with the nuclear envelope (NE) remodeling. In a so-called 'open' mitosis the envelope of the mother nucleus is dismantled allowing the cytoplasmic spindle microtubules to capture the chromosomes. Alternatively, cells undergoing 'closed' mitosis assemble the intranuclear spindle and divide the nucleus without ever losing the nucleocytoplasmic compartmentalization. Here we focus on the mechanisms underlying mitotic NE dynamics in unicellular eukaryotes undergoing a closed nuclear division, paying specific attention to the emerging roles of the lipid biosynthesis machinery in this process. We argue that lessons learned in these organisms may be generally relevant to understanding the NE remodeling and the evolution of mitotic mechanisms throughout the eukaryotic domain.

The Nek6 and Nek7 protein kinases are required for robust mitotic spindle formation and cytokinesis

Nek6 and Nek7 are members of the NIMA-related serine/threonine kinase family. Previous work showed that they contribute to mitotic progression downstream of another NIMA-related kinase, Nek9, although the roles of these different kinases remain to be defined. Here, we carried out a comprehensive analysis of the regulation and function of Nek6 and Nek7 in human cells. By generating specific antibodies, we show that both Nek6 and Nek7 are activated in mitosis and that interfering with their activity by either depletion or expression of reduced-activity mutants leads to mitotic arrest and apoptosis. Interestingly, while completely inactive mutants and small interfering RNA-mediated depletion delay cells at metaphase with fragile mitotic spindles, hypomorphic mutants or RNA interference treatment combined with a spindle assembly checkpoint inhibitor delays cells at cytokinesis. Importantly, depletion of either Nek6 or Nek7 leads to defective mitotic progression, indicating that although highly similar, they are not redundant. Indeed, while both kinases localize to spindle poles, only Nek6 obviously localizes to spindle microtubules in metaphase and anaphase and to the midbody during cytokinesis. Together, these data lead us to propose that Nek6 and Nek7 play independent roles not only in robust mitotic spindle formation but also potentially in cytokinesis.

Copy number suppressors of the Aspergillus nidulans nimA1 mitotic kinase display distinctive and highly dynamic cell cycle-regulated locations

The Aspergillus nidulans NIMA kinase is essential for mitosis and is the founding member of the conserved NIMA-related kinase (Nek) family of protein kinases. To gain insight into NIMA function, a copy number suppression screen has been completed that defines three proteins termed MCNA, MCNB, and MCNC (multi-copy-number suppressor of nimA1 A, B, and C). All display a distinctive and dynamic cell cycle-specific distribution. MCNC has weak similarity to Saccharomyces cerevisiae Def1 within a shared CUE-like domain. MCNC, like Def1, is a cytoplasmic protein with slow mobility during sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and its deletion causes polarization defects and a small colony phenotype. MCNC enters nuclei during mitosis. In contrast, MCNB is a nuclear protein displaying increased nuclear levels as cells progress through interphase but is lost from nuclei at mitosis. MCNB is highly related to the Schizosaccharomyces pombe forkhead transcription factor Sep1 and is likely a transcriptional activator of nimA. Most surprisingly, MCNA, a protein restricted to the aspergilli and pathogenic systemic dimorphic fungi (the Eurotiomycetes), defines a nuclear body located near nucleoli at the nuclear periphery of G(2) nuclei. During progression through mitosis, the MCNA body is excluded from nuclei. Cytoplasmic MCNA bodies then diminish during early stages of interphase, and single MCNA bodies are formed within nuclei as interphase progresses. Three sites of MCNA phosphorylation were mapped and mutated to implicate proline-directed phosphorylation in the equal segregation of MCNA during the cell cycle. The data indicate all three MCN proteins likely have cell cycle functions.

The cell cycle and Toxoplasma gondii cell division: tightly knit or loosely stitched?

The flexibility displayed by apicomplexan parasites to vary their mode of replication has intrigued biologists since their discovery by electron microscopy in the 1960s and 1970s. Starting in the 1990s we began to understand the cell biology of the cytoskeleton elements driving cytokinesis. By contrast, the molecular mechanisms that regulate the various division modes and how they translate into the budding process that uniquely characterizes this parasite family are much less understood. Although growth mechanisms are a neglected area of study, it is an important pathogenic parameter as fast division rounds are associated with fulminant infection whereas slower growth attenuates virulence, as is exploited in some vaccine strains. In this review we summarize a recent body of cell biological experiments that are rapidly leading to an understanding of the events that yield successful mitosis and cytokinesis in Toxoplasma. We place these observations within a cell cycle context with comments on how these events may be regulated by known eukaryotic checkpoints active in fission and budding yeasts as well as mammalian cells. The presence of cell cycle control mechanisms in the Apicomplexa is supported by our findings that identify several cell cycle checkpoints in Toxoplasma. The progress of the cell cycle is ultimately controlled by cyclin-Cdk pair activities, which are present throughout the Apicomplexa. Although many of the known controllers of cyclin-Cdk activity are present, several key controls cannot readily be identified, suggesting that apicomplexan parasites deviate at these points from the higher eukaryotic models. Altogether, new insights in Toxoplasma replication are reciprocally applied to hypothesize how other division modes in the Toxoplasma life cycle and in other Apicomplexa species could be controlled in terms of cell cycle checkpoint regulation.

Mitotic regulation by NIMA-related kinases

The NIMA-related kinases represent a family of serine/threonine kinases implicated in cell cycle control. The founding member of this family, the NIMA kinase of Aspergillus nidulans, as well as the fission yeast homologue Fin1, contribute to multiple aspects of mitotic progression including the timing of mitotic entry, chromatin condensation, spindle organization and cytokinesis. Mammals contain a large family of eleven NIMA-related kinases, named Nek1 to Nek11. Of these, there is now substantial evidence that Nek2, Nek6, Nek7 and Nek9 also regulate mitotic events. At least three of these kinases, as well as NIMA and Fin1, have been localized to the microtubule organizing centre of their respective species, namely the centrosome or spindle pole body. Here, they have important functions in microtubule organization and mitotic spindle assembly. Other Nek kinases have been proposed to play microtubule-dependent roles in non-dividing cells, most notably in regulating the axonemal microtubules of cilia and flagella. In this review, we discuss the evidence that NIMA-related kinases make a significant contribution to the orchestration of mitotic progression and thereby protect cells from chromosome instability. Furthermore, we highlight their potential as novel chemotherapeutic targets.

Fission yeast Rnf4 homologs are required for DNA repair

We describe two RING finger proteins in the fission yeast Schizosaccharomyces pombe, Rfp1 and Rfp2. We show that these proteins function redundantly in DNA repair. Rfp1 was isolated as a Chk1-interacting protein in a two-hybrid screen and has high amino acid sequence similarity to Rfp2. Deletion of either gene does not cause a phenotype, but a double deletion (rfp1Deltarfp2Delta) showed poor viability and defects in cell cycle progression. These cells are also sensitive to DNA-damaging agents, although they maintained normal checkpoint signaling to Chk1. Rfp1 and Rfp2 are most closely related to human Rnf4, and we showed that Rnf4 can substitute functionally for Rfp1 and/or Rfp2. The double mutants also showed significantly increased levels of protein SUMOylation, and we identified an S. pombe Ulp2/Smt4 homolog that, when overexpressed, reduced SUMO levels and suppressed the DNA damage sensitivity of rfp1Delta rfp2Delta cells.

Phosphorylation of histone H3 in plants--a dynamic affair

Histones are the main protein components of chromatin: they undergo extensive post-translational modifications, particularly acetylation, methylation, phosphorylation, ubiquitination and ADP-ribosylation which modify the structural/functional properties of chromatin. Post-translational modifications of the N-terminal tails of the core histones within the nucleosome particle are thought to act as signals from the chromatin to the cell, for various processes. Thus, in many ways histone tails can be viewed as complex protein-protein interaction surfaces that are regulated by numerous post-translational modifications. Histone phosphorylation has been linked to chromosome condensation/segregation, activation of transcription, apoptosis and DNA damage repair. In plants, the cell cycle dependent phosphorylation of histone H3 has been described; it is hyperphosphorylated at serines 10/28 and at threonines 3/11 during both mitosis and meiosis in patterns that are specifically coordinated in both space and time. Although this post-translational modification is highly conserved, data show that the chromosomal distribution of individual modifications can differ between groups of eukaryotes. Initial results indicate that members of the plant Aurora kinase family have the capacity to control cell cycle regulated histone H3 phosphorylation, and in addition we describe other potential H3 kinases and discuss their functions.

Nek7 kinase is enriched at the centrosome, and is required for proper spindle assembly and mitotic progression

Members of the NIMA-related kinases (NRK) family are recently emerging as central regulators of various aspects of the cell cycle. However, the cellular roles of the mammalian NRK, Nek7, remain obscure. We show here that the endogenous Nek7 protein is enriched at the centrosome in a microtubule-independent manner. Overexpression of wt or kinase-defective Nek7 resulted in cells of rounder appearance, and higher proportions of multinuclear and apoptotic cells. Down-regulation of Nek7 using a small interfering RNA approach resulted in a significant increase in mitotic cells presenting multipolar spindle phenotype. These results suggest a role for Nek7 in regulating proper spindle assembly and mitotic progression.

Regulation of gene expression and cell division by Polo-like kinases

Much scientific research has focused on characterising regulatory pathways and mechanisms responsible for cell integrity, growth and division. This area of study is of direct relevance to human medicine as uncontrolled growth and division underlies many diseases, most strikingly cancer. In cancer cells, normal regulatory mechanisms for growth and division are often altered, or even fail to exist. This review summarises the mechanisms that control the genes and gene products regulating cytokinesis and cell separation in the fission yeast Schizosaccharomyces pombe, as well as highlighting conserved aspects in the budding yeast Saccharomyces cerevisiae and higher eukaryotes. Particular emphasis is put on the role of gene expression, the Polo-like kinases (Plks), and the signal transduction pathways that control these processes.

Caught Nek-ing: cilia and centrioles

The Nek family of cell-cycle kinases is widely represented in eukaryotes and includes numerous proteins that were described only recently and remain poorly characterized. Comparing Neks in the context of clades allows us to examine the question of whether microbial eukaryotic Neks, although not strictly orthologs of their vertebrate counterparts, can provide clues to ancestral functions that might be retained in the vertebrate Neks. Relatives of the Nek2/NIMA proteins play important roles at the G2-M transition in nuclear envelope breakdown and centromere separation. Nek6, Nek7 and Nek9 also seem to regulate mitosis. By contrast, Nek1 and Nek8 have been linked with polycystic kidney disease. Results of statistical analysis indicate that the family coevolved with centrioles that function as both microtubule-organizing centers and the basal bodies of cilia. This evolutionary perspective, taken together with functional studies of microbial Neks, provides new insights into the cellular roles of the proteins and disease with which some of them have been linked.

Potential link between the NIMA mitotic kinase and nuclear membrane fission during mitotic exit in Aspergillus nidulans

We have isolated TINC as a NIMA-interacting protein by using the yeast two-hybrid system and have confirmed that TINC interacts with NIMA in Aspergillus nidulans. The TINC-NIMA interaction is stabilized in the absence of phosphatase inhibitors and in the presence of kinase-inactive NIMA, suggesting that the interaction is enhanced when NIMA is not fully activated. TINC is a cytoplasmic protein. TINC homologues and a TINC-like protein (A. nidulans HETC) are conserved in other filamentous fungi. Neither deletion of tinC nor deletion of both tinC and A. nidulans hetC is lethal, but deletion of tinC does produce cold sensitivity as well as osmotic sensitivity. Expression of an amino-terminal-truncated form of TINC (DeltaN-TINC) inhibits colony growth in Aspergillus and localizes to membrane-like structures within the cell. Examination of cell cycle progression in these cells reveals that they progress through multiple defective mitoses. Many cells contain large polyploid single nuclei, while some appear to have separated masses of DNA. Examination of the nuclear envelopes of cells containing more than one DNA mass reveals that both DNA masses are contained within a single nuclear envelope, indicating that nuclear membrane fission is defective. The ability of these cells to separate DNA segregation from nuclear membrane fission suggests that this coordination is normally a regulated process in A. nidulans. Additional experiments demonstrate that expression of DeltaN-TINC results in premature NIMA disappearance in mitotic samples. We propose that TINC's interaction with NIMA and the cell cycle defects produced by DeltaN-TINC expression suggest possible roles for TINC and NIMA during nuclear membrane fission.

Cyclophilin nomenclature problems, or, 'a visit from the sequence police'

Why is agreement on one particular name for each gene important? As one genome after another becomes sequenced, it is imperative to consider the complexity of genes, genetic architecture, gene expression, gene-gene and gene-product interactions and evolutionary relatedness across species. To agree on a particular gene name not only makes one's own research easier, it aids automated text-mining algorithms and search engines, which are increasingly employed to find relationships in the millions of abstracts in the medical research literature and sequence databases. A common nomenclature system will also be helpful to the present generation, as well as future generations, of graduate students and postdoctoral fellows who are about to enter genomics research. In this paper, the authors present some problems that arose when two separate research communities decided to choose the same root, CYP, for naming their gene families. They then offer a logical solution, by renaming the cyclophilin genes with a common root, such a cyn- in Caenorhabditis and CYN- in mammals (Cyn in mouse), and using evolutionary divergence to cluster genes of the highest level of relatedness.

Identification of cell cycle-regulated genes in fission yeast

Cell cycle progression is both regulated and accompanied by periodic changes in the expression levels of a large number of genes. To investigate cell cycle-regulated transcriptional programs in the fission yeast Schizosaccharomyces pombe, we developed a whole-genome oligonucleotide-based DNA microarray. Microarray analysis of both wild-type and cdc25 mutant cell cultures was performed to identify transcripts whose levels oscillated during the cell cycle. Using an unsupervised algorithm, we identified 747 genes that met the criteria for cell cycle-regulated expression. Peaks of gene expression were found to be distributed throughout the entire cell cycle. Furthermore, we found that four promoter motifs exhibited strong association with cell cycle phase-specific expression. Examination of the regulation of MCB motif-containing genes through the perturbation of DNA synthesis control/MCB-binding factor (DSC/MBF)-mediated transcription in arrested synchronous cdc10 mutant cell cultures revealed a subset of functional targets of the DSC/MBF transcription factor complex, as well as certain gene promoter requirements. Finally, we compared our data with those for the budding yeast Saccharomyces cerevisiae and found approximately 140 genes that are cell cycle regulated in both yeasts, suggesting that these genes may play an evolutionarily conserved role in regulation of cell cycle-specific processes. Our complete data sets are available at http://giscompute.gis.a-star.edu.sg/~gisljh/CDC.

Cell cycle-regulated transcription in fission yeast

A fundamental process in biology is the mechanism by which cells duplicate and divide to produce two identical daughter cells. The fission yeast, Schizosaccharomyces pombe, has proved to be an excellent model organism to study the role that gene expression plays in this process. The basic paradigm emerging is that a number of groups of genes are expressed in successive waves at different cell cycle times. Transcription of a particular group is controlled by a common DNA motif present in each gene's promoter, bound by a transcription factor complex. Each motif and transcription factor complex is specific to the time in the cell cycle when the group of genes is expressed. Examples of this are the MBF (MCB-binding factor)/MCB (MluI cell cycle box) system controlling gene expression at the start of S-phase, and PBF (PCB-binding factor)/PCB (Pombe cell cycle box) regulation of transcription at the end of mitosis. In some cases, these transcription control systems also operate during the alternative form of cell division, meiosis.

Recruitment of NIMA kinase shows that maturation of the S. pombe spindle-pole body occurs over consecutive cell cycles and reveals a role for NIMA in modulating SIN activity

Mitotic exit in Saccharomyces cerevisiae and septation in Schizosaccharomyces pombe are regulated by a conserved signaling network called the mitotic exit and septum initiation networks (SIN), respectively. The network is active on one of the two anaphase B spindle-pole bodies (SPBs). Whereas the inherent asymmetry of growth by budding accounts for elements of the asymmetry in S. cerevisiae, it has been unclear how, or why, the pathway is asymmetric in S. pombe. We show that elements of SPB duplication in S. pombe are conservative, and that the SIN is active on the new SPB. SIN association with the new SPB persists after transient depolymerization of microtubules. The localization of the NIMA-related kinase, Fin1, reveals further complexity in SPB inheritance. Fin1 associates with the SPB bearing the older components in all cells and with the "new" SPB in half of the population. Fin1 only binds the new SPB when this new SPB has arisen from the duplication of an SPB that is two or more cycles old. Thus, each of the four SPBs generated over two consecutive cell cycles are different, because they have distinct fates in the next cell cycle. Fin1 binds the SPB once the SIN is active and the association requires the SIN inhibitors Byr4 and Cdc16. Fin1 physically associates with Byr4. Compromising Fin1 function leads to SIN activation on both anaphase B SPBs and promotes septation, indicating that Fin1 restrains SIN activity on the old SPB.

Arabidopsis kinome: after the casting

Arabidopsis thaliana is used as a favourite experimental organism for many aspects of plant biology. We capitalized on the recently available Arabidopsis genome sequence and predicted proteome, to draw up a genome-scale protein serine/threonine kinase (PSTK) inventory. The PSTKs represent about 4% of the A. thaliana proteome. In this study, we provide a description of the content and diversity of the non-receptor PSTKs. These kinases have crucial functions in sensing, mediating and coordinating cellular responses to an extensive range of stimuli. A total of 369 predicted non receptor PSTKs were detailed: the Raf superfamily, the CMGC, CaMK, AGC and STE families, as well as a few small clades and orphan sequences. An extensive relationship analysis of these kinases allows us to classify the proteins in superfamilies, families, sub-families and groups. The classification provides a better knowledge of the characteristics shared by the different clades. We focused on the MAP kinase module elements, with particular attention to their docking sites for protein-protein interaction and their biological function. The large number of A. thaliana genes encoding kinases might have been achieved through successive rounds of gene and genome duplications. The evolution towards an increasing gene number suggests that functional redundancy plays an important role in plant genetic robustness.

The SONBNUP98 Nucleoporin Interacts With the NIMA Kinase in Aspergillus nidulans

The Aspergillus nidulans NIMA kinase is essential for mitotic entry. At restrictive temperature, temperature-sensitive nimA alleles arrest in G2, before accumulation of NIMA in the nucleus. We performed a screen for extragenic suppressors of the nimA1 allele and isolated two cold-sensitive son (suppressor of nimA1) mutants. The sonA1 mutant encoded a nucleoporin that is a homolog of yeast Gle2/Rae1. We have now cloned SONB, a second nucleoporin genetically interacting with NIMA. sonB is essential and encodes a homolog of the human NUP98/NUP96 precursor. Similar to NUP98/NUP96, SONBNUP98/NUP96 is autoproteolytically cleaved to generate SONBNUP98 and SONBNUP96. SONBNUP98 localizes to the nuclear pore complex and contains a GLEBS domain (Gle2 binding sequence) that binds SONAGLE2. A point mutation within the GLEBS domain of SONB1NUP98 suppresses the temperature sensitivity of the nimA1 allele and compromises the physical interaction between SONAGLE2 and SONB1NUP98. The sonB1 mutation also causes sensitivity to hydroxyurea. We isolated the histone H2A-H2B gene pair as a copy-number suppressor of sonB1 cold sensitivity and hydroxyurea sensitivity. The data suggest that the nucleoporins SONAGLE2 and SONBNUP98 and the NIMA kinase interact and regulate nuclear accumulation of mitotic regulators to help promote mitosis.

TINA interacts with the NIMA kinase in Aspergillus nidulans and negatively regulates astral microtubules during metaphase arrest

The tinA gene of Aspergillus nidulans encodes a protein that interacts with the NIMA mitotic protein kinase in a cell cycle-specific manner. Highly similar proteins are encoded in Neurospora crassa and Aspergillus fumigatus. TINA and NIMA preferentially interact in interphase and larger forms of TINA are generated during mitosis. Localization studies indicate that TINA is specifically localized to the spindle pole bodies only during mitosis in a microtubule-dependent manner. Deletion of tinA alone is not lethal but displays synthetic lethality in combination with the anaphase-promoting complex/cyclosome mutation bimE7. At the bimE7 metaphase arrest point, lack of TINA enhanced the nucleation of bundles of cytoplasmic microtubules from the spindle pole bodies. These microtubules interacted to form spindles joined in series via astral microtubules as revealed by live cell imaging. Because TINA is modified and localizes to the spindle pole bodies at mitosis, and lack of TINA causes enhanced production of cytoplasmic microtubules at metaphase arrest, we suggest TINA is involved in negative regulation of the astral microtubule organizing capacity of the spindle pole bodies during metaphase.

Never say never. The NIMA-related protein kinases in mitotic control

Mitosis sees a massive reorganization of cellular architecture. The microtubule cytoskeleton is reorganized to form a bipolar spindle between duplicated microtubule organizing centers, the chromosomes are condensed, attached to the spindle at their kinetochores, and, through the action of multiple molecular motors, the chromosomes are segregated into two daughter cells. Mitosis also sees a substantial wave of protein phosphorylation, controlling signaling events that coordinate mitotic processes and ensure accurate chromosome segregation. The key switch for the onset of mitosis is the archetypal cyclin-dependent kinase, Cdc2. Under the direction of Cdc2 is an executive of protein serine/threonine kinases that fall into three families: the Polo kinases, Aurora kinases and the NIMA-related kinases (Nrk). The latter family has proven the most enigmatic in function, although recent advances from several sources are beginning to reveal a common functional theme.

A new identity for MLK3 as an NIMA-related, cell cycle-regulated kinase that is localized near centrosomes and influences microtubule organization

Although conserved counterparts for most proteins involved in the G(2)/M transition of the cell cycle have been found in all eukaryotes, a notable exception is the essential but functionally enigmatic fungal kinase NIMA. While a number of vertebrate kinases have been identified with catalytic domain homology to NIMA, none of these resemble NIMA within its extensive noncatalytic region, a region critical for NIMA function in Aspergillus nidulans. We used a bioinformatics approach to search for proteins with homology to the noncatalytic region of NIMA and identified mixed lineage kinase 3 (MLK3). MLK3 has been proposed to serve as a component in MAP kinase cascades, particularly those resulting in the activation of the c-Jun N-terminal kinase (JNK). Here we describe the first in-depth study of endogenous MLK3 and report that, like NIMA, MLK3 phosphorylation and activity are enhanced during G(2)/M, whereas JNK remains inactive. Coincident with the G(2)/M transition, a period marked by dramatic reorganization of the cytoplasmic microtubule network, endogenous MLK3 transiently disperses away from the centrosome and centrosomal-proximal sites where it is localized during interphase. Furthermore, when overexpressed, MLK3, like NIMA, localizes to the centrosomal region, induces profound disruption of cytoplasmic microtubules and a nuclear distortion phenotype that differs from mitotic chromosome condensation. Cellular depletion of MLK3 protein using siRNA technology results in an increased sensitivity to the microtubule-stabilizing agent taxol. Our studies suggest a new role for MLK3, separable from its function in the JNK pathway, that may contribute to promoting microtubule instability, a hallmark of M phase entry.

Nek11, a new member of the NIMA family of kinases, involved in DNA replication and genotoxic stress responses

DNA replication and genotoxic stresses activate various checkpoint-associated protein kinases, and checkpoint dysfunction often leads to cell lethality. Here, we have identified new members of the mammalian NIMA family of kinases, termed Nek11L and Nek11S (NIMA-related kinase 11 Long and Short isoform) as novel DNA replication/damage stresses-responsive kinases. Molecular cloning and biochemical studies showed that the catalytic domain of Nek11 is most similar to Nek4 and Nek3, and substrate specificity of Nek11L is distinguishable from those of NIMA and Nek2. The expression of nek11L mRNA increased through S to G(2)/M phase, and subcellular localization of Nek11 protein altered between interphase and prometaphase, suggesting multiple roles of Nek11. We found an activation of Nek11 kinase activity when cells were treated with various DNA-damaging agents and replication inhibitors, and this activation of Nek11 was suppressed by caffeine in HeLaS3 cells. The transient expression of wild-type Nek11L enhanced the aphidicolin-induced S-phase arrest, whereas the aphidicolin-induced S-phase arrest was reduced in the U2OS cell lines expressing kinase-negative Nek11L (K61R), and these cells were more sensitive to aphidicolin-induced cell lethality. Collectively, these results suggest that Nek11 has a role in the S-phase checkpoint downstream of the caffeine-sensitive pathway.

The Nek2 protein kinase: a novel regulator of centrosome structure

Regulation of the centrosome, the major microtubule organizing centre in an animal cell, is in large part controlled by cell cycle-dependent protein phosphorylation. Along with cyclin dependent kinases, polo kinases and Aurora kinases, NIMA-related kinases are emerging as critical regulators of centrosome structure and function. Nek2 is the most closely related vertebrate protein by sequence to the essential mitotic regulator NIMA of Aspergillus nidulans. Nek2 is highly enriched at the centrosome and functional studies in human and Xenopus systems support a role for Nek2 in both maintenance and modulation of centrosome architecture. In particular, current evidence supports a model in which one function of Nek2 kinase activity is to promote the splitting of duplicated centrosomes at the onset of mitosis through phosphorylation of core centriolar proteins. Recent studies in lower organisms have raised the possibility that kinases related to Nek2 may have conserved functions in MTOC organization, as well as in other aspects of mitotic progression.

Schizosaccharomyces pombe NIMA-related kinase, Fin1, regulates spindle formation and an affinity of Polo for the SPB

The Aspergillus nidulans protein kinase NIMA regulates mitotic commitment, while the human and Xenopus equivalents influence centrosome function. Two recessive, temperature-sensitive mutations in the Schizosaccharomyces pombe NIMA homologue, Fin1, blocked spindle formation at 37 degrees C. One of the two spindle pole bodies (SPBs) failed to nucleate microtubules. This phenotype was reduced by accelerating mitotic commitment through genetic inhibition of Wee1 or activation of either Cdc25 or Cdc2. Polo kinase (Plo1) normally associates with the SPB of mitotic, but not interphase cells. cut12.s11 is a dominant mutation in an SPB component that both suppresses cdc25 mutants and promotes Plo1 association with the interphase SPB. Both cut12.s11 phenotypes were abolished by removing Fin1 function. Elevating Fin1 levels promoted Plo1 recruitment to the interphase SPB of wild-type cells and reduced the severity of the cdc25.22 phenotype. These data are consistent with Fin1 regulating Plo1 function during mitotic commitment. The fin1 mitotic commitment and spindle phenotypes resemble distinct nimA phenotypes in different systems and suggest that the function of this family of kinases may be conserved across species.