Phase-specific Proteins Research Articles

Cyclin-Dependent Kinases and CTD Phosphatases in Cell Cycle Transcriptional Control: Conservation across Eukaryotic Kingdoms and Uniqueness to Plants.

Cell cycle control is vital for cell proliferation in all eukaryotic organisms. The entire cell cycle can be conceptually separated into four distinct phases, Gap 1 (G1), DNA synthesis (S), G2, and mitosis (M), which progress sequentially. The precise control of transcription, in particular, at the G1 to S and G2 to M transitions, is crucial for the synthesis of many phase-specific proteins, to ensure orderly progression throughout the cell cycle. This mini-review highlights highly conserved transcriptional regulators that are shared in budding yeast (Saccharomyces cerevisiae), Arabidopsis thaliana model plant, and humans, which have been separated for more than a billion years of evolution. These include structurally and/or functionally conserved regulators cyclin-dependent kinases (CDKs), RNA polymerase II C-terminal domain (CTD) phosphatases, and the classical versus shortcut models of Pol II transcriptional control. A few of CDKs and CTD phosphatases counteract to control the Pol II CTD Ser phosphorylation codes and are considered critical regulators of Pol II transcriptional process from initiation to elongation and termination. The functions of plant-unique CDKs and CTD phosphatases in relation to cell division are also briefly summarized. Future studies towards testing a cooperative transcriptional mechanism, which is proposed here and involves sequence-specific transcription factors and the shortcut model of Pol II CTD code modulation, across the three eukaryotic kingdoms will reveal how individual organisms achieve the most productive, large-scale transcription of phase-specific genes required for orderly progression throughout the entire cell cycle.

Exploring Packaged Microvesicle Proteome Composition of Chinese Hamster Ovary Secretome

Background: Chinese Hamster Ovary cells (CHO) are the most preferred host cells to meet the increasing demand for high quality ‘human-like’ complex biologics production, but is faced with the challenge of achieving high yield at an affordable price. Secreted proteins critically impact cell growth and product quality and quantity and an integral part of secretome is the packaged microvesicles. In spite of numerous efforts to characterize spent-media proteome, none have identified specific contribution of microvesicles, necessitating further differential analysis of these defined fractions of spent-media proteome, specifically packaged microvesicles. Methods: We have investigated proteome of microvesicles isolated from lag, log, stationary and death phase of CHO batch culture using LC-MS/MS based-proteomic approach to identify proteins that may be involved in regulation of cell growth, viability and productivity in culture. Results: A total of 89 unique proteins were identified in the microvesicles isolated from lag, log, stationary and death-phase of culture; of these only 8.9% were categorized as secretory proteins leaving ~91% proteins of intracellular and non-secretory nature. Microvesicles were observed to contain a number of culture phase-specific proteins which included cell-signaling molecules, transcription and translation regulators and molecular chaperons; many of which are known growth regulators, indicating the potency of microvesicles in regulating culture health. Conclusions: This is the first report of CHO microvesicular proteome and this knowledge is critical in developing rationale design of perfusion process, downstream purification process for rendering improved product stability and also novel cell engineering approaches to maximize growth and improved media formulations to maximize yield and minimize product degradation.

Life Stage-specific Proteomes of Legionella pneumophila Reveal a Highly Differential Abundance of Virulence-associated Dot/Icm effectors

Major differences in the transcriptional program underlying the phenotypic switch between exponential and post-exponential growth of Legionella pneumophila were formerly described characterizing important alterations in infection capacity. Additionally, a third state is known where the bacteria transform in a viable but nonculturable state under stress, such as starvation. We here describe phase-related proteomic changes in exponential phase (E), postexponential phase (PE) bacteria, and unculturable microcosms (UNC) containing viable but nonculturable state cells, and identify phase-specific proteins. We present data on different bacterial subproteomes of E and PE, such as soluble whole cell proteins, outer membrane-associated proteins, and extracellular proteins. In total, 1368 different proteins were identified, 922 were quantified and 397 showed differential abundance in E/PE. The quantified subproteomes of soluble whole cell proteins, outer membrane-associated proteins, and extracellular proteins; 841, 55, and 77 proteins, respectively, were visualized in Voronoi treemaps. 95 proteins were quantified exclusively in E, such as cell division proteins MreC, FtsN, FtsA, and ZipA; 33 exclusively in PE, such as motility-related proteins of flagellum biogenesis FlgE, FlgK, and FliA; and 9 exclusively in unculturable microcosms soluble whole cell proteins, such as hypothetical, as well as transport/binding-, and metabolism-related proteins. A high frequency of differentially abundant or phase-exclusive proteins was observed among the 91 quantified effectors of the major virulence-associated protein secretion system Dot/Icm (> 60%). 24 were E-exclusive, such as LepA/B, YlfA, MavG, Lpg2271, and 13 were PE-exclusive, such as RalF, VipD, Lem10. The growth phase-related specific abundance of a subset of Dot/Icm virulence effectors was confirmed by means of Western blotting. We therefore conclude that many effectors are predominantly abundant at either E or PE which suggests their phase specific function. The distinct temporal or spatial presence of such proteins might have important implications for functional assignments in the future or for use as life-stage specific markers for pathogen analysis.

Histone Deacetylase Inhibitors Induce Differentiation of Human Endometrial Adenocarcinoma Cells through Up-Regulation of Glycodelin

Histone reversible acetylation, which is controlled by histone acetyltransferases and deacetylases, plays a fundamental role in gene transcription. Histone deacetylase inhibitors (HDACIs), such as trichostatin A (TSA) and suberoylanilide hydroxamic acid (SAHA), have been characterized not only as anticancer drugs, but also as cytodifferentiation-inducing agents. In human endometrium, postovulatory production of progesterone directs estrogen-primed endometrial glandular cells to differentiate and thereby produce a number of unique bioactive substances, including glycodelin, that are critical for implantation at the secretory phase of the menstrual cycle. In this study, we show that TSA and SAHA, belonging to the hydroxamic acid group of HDACIs, can induce the phenotype of a human endometrial adenocarcinoma cell line, Ishikawa (originally derived from the glandular component of the endometrium), to differentiate to closely resemble normal endometrial epithelium in a time- and dose-dependent manner, as determined by morphological changes, synthesis of glycogen, and expression of secretory phase-specific proteins, including glycodelin. The proliferation- and differentiation-modulating effects elicited by TSA and SAHA at their optimal concentrations were comparable or more potent than those exerted by combined treatment with progesterone and estradiol. Furthermore, the gene silencing of glycodelin by small interference RNA resulted in the blockade of HDACI-induced differentiation in Ishikawa cells, suggesting the requirement for glycodelin for endometrial epithelial differentiation. Our results collectively indicate that TSA and SAHA are potent differentiation inducers for endometrial glandular cells, providing a clue for a possible therapeutic strategy to modulate endometrial function by targeting glycodelin.

Proteomic study of a model causative agent of harmful algal blooms, Prorocentrum triestinum II: the use of differentially expressed protein profiles under different growth phases and growth conditions for bloom prediction.

Simultaneous comparison of differentially expressed protein profiles of Prorocentrum triestinum grown under different growth phases and growth conditions indicated the presence of phase-specific and stress-responsive proteins, respectively. Correlation studies on these proteins in relation to cell division phasing patterns and to models of phytoplankton growth inferred the possible functions. Most notable among these proteins were groups of proteins thought to trigger or mediate cells through specific phases of division of this alga, e.g., BP1, BP2, PB1, PB2, and PB3. Other proteins (e.g., group 1 proteins) thought to be responsible for maintaining and supporting cell concentration under adverse conditions were found. Furthermore, another group of proteins (group 2 proteins) thought to be stress-responsive were also detected. Taken overall, these differentially expressed proteins provided important information for uncovering various protective and adaptive mechanisms in the dinoflagellate's life cycle. These proteins have the potential to serve as "indicator proteins" for rapid assessment of the nutritional or metabolic status of these phytoplankton cells,and monitoring the differential expression of these phase-specific proteins and stress-specific proteins could be an important biomarker for bloom prediction.

S phase-specific DNA-binding proteins interacting with the Hex and Oct motifs in type I element of the wheat histone H3 promoter.

The type I element (CCACGTCANCGATCCGCG), consisting of the Hex motif (CCACGTCA) and the reverse-oriented Oct motif (GATCCGCG), is necessary and sufficient to confer the S phase-specific transcription of the wheat histone H3 (TH012) gene. The transcriptional regulation via the type I element is thought to occur through interactions between transcription factors which bind specifically to the Hex and Oct motifs. Here we report S phase-specific DNA-binding proteins interacting with the type I element in partially synchronized wheat cultured cells. Hex motif-binding proteins found here resembled HBP-1a, as reported previously in terms of DNA-binding specificity. DNA-binding activities of the HBP-1a-like proteins were modulated by phosphorylation/dephosphorylation. In the electrophoretic mobility shift assay of the wheat nuclear extract, we also found three Oct motif-specific binding proteins, named OBRF (octamer-binding regulatory factor)-1, -2 and -3. One of the HBP-1a-like proteins and OBRF-1 appeared predominantly at the S phase. Thus, it was supposed that these two factors play a crucial role in the S phase-specific regulation of wheat histone gene expression.

Phase-Specific Protein Expression in the Dimorphic YeastSaccharomyces cerevisiae

In oxygen-limited continuous culture,Saccharomyces cerevisiaeformed pseudohyphae by unipolar budding. We developed a continuous cultivation sequence to discriminate phase-specific from metabolically regulated proteins during dimorphism. Computer-aided substractive analysis of 2D–PAGE protein patterns allowed the detection of proteins specifically expressed during yeast and pseudohyphal phases. Image analysis resolved 3 spots that were specific to the pseudohyphal phase and 2 spots that were specific to yeast phase. In addition to phase-specific proteins, important regulation of protein expression took place. A group of 9 proteins was highly over-expressed during the yeast phase when another group of 12 was under-expressed. This phenomenon was reversed during the pseudohyphal phase. These experiments showed that dimorphism inS. cerevisiaeis associated with the expression of specific proteins and suggest that yeast phase-specific proteins maintain the yeast form or repress pseudohyphae formation.

Milk Composition in a Field Population of Red Kangaroos, Macropus Rufus (Desmarest) (Macropodidae: Marsupialia)

The composition of milk from early pouch life (0-40 days) to weaning (360 days) was determined in samples collected from a field population of red kangaroos, Macropus rufus (n = 150). Total milk solids increased from 11% at 0-40 days to 26% at permanent emergence from the pouch (235 days), then decreased towards weaning. Compared with other macropodids, milk from red kangaroos is relatively dilute. Carbohydrate concentrations increased from 2.0 to 6.2% at about Day 235 then declined while lipid concentrations increased from 3.9 to 10.3% over the course of lactation. Protein values increased from 5.0 to 7.0% prior to pouch emergence. Whey proteins were separated by means of SDS PAGE, identifying and confirming the presence of several phase-specific proteins. These results are similar to those reported for components of milk in captive red kangaroos and therefore confirm the general macropodid pattern of changing milk composition throughout lactation for a field population of red kangaroos.

Biochemical and morphological characterization of the nuclear matrix during the synchronous cell cycle of Physarum polycephalum.

We have investigated biochemical and ultrastructural aspects of the nuclear matrix during the naturally synchronous cell cycle of Physarum polycephalum. The morphology of the in situ nuclear matrix exhibited significant cell cycle changes as revealed by electron microscopic examination, especially during the progression of nuclei through mitosis and S-phase. In mitosis the interchromatin matrix was found to be retracted to the nuclear periphery; during S-phase this interchromatin matrix gradually resembled, concomitant with the reconstruction of a nucleolar remnant structure. During the G2-period no significant changes in matrix morphology were observed. The pattern of nuclear matrix proteins was invariant during the cell cycle; no cycle phase-specific proteins could be detected. In vivo labelling of plasmodia with [35S]methionine/cysteine showed that only a few proteins are synthesized and assembled into nuclear matrix structures in a cell cycle-dependent way; the majority of proteins were synthesized almost continuously. This was also shown for nuclear lamins homologues. In contrast to bulk nuclear histones, those histones that remain tightly bound to the nuclear matrix were synthesized and assembled into nuclear structures in the very first hour of S-phase; assembly was terminated in mid-S-phase, indicating that nuclear matrix-bound chromatin is replicated early in S-phase. Comparison of the acetylation pattern of matrix-bound histone H4 with bulk nuclear H4 revealed a largely elevated acetate content of matrix H4. The percentage of acetylated subspecies was entirely different from that in bulk nuclear H4, indicating that matrix-associated histones represent a subpopulation of nuclear histones with distinct properties, reflecting specific structural requirements of matrix-attached chromatin.

Cyclin E/cdk2 and cyclin A/cdk2 kinases associate with p107 and E2F in a temporally distinct manner.

Cyclin E is classified as a putative G1 cyclin on the basis of its cyclic pattern of mRNA expression, with maximal levels being detected near the G1/S boundary. We report here that cyclin E is found associated with the transcription factor E2F in a temporally regulated fashion. E2F is known to be a critical transcription factor for the expression of some S phase-specific proteins and is thought to be important for a series of others. Antisera specific for cyclin E were raised and used to demonstrate an association between cyclin E and E2F. This cyclin E/E2F complex was seen in a variety of human cell lines from various tissues, but its appearance was detected primarily during the G1 phase of the cell cycle. The cyclin E/E2F association decreased as cells entered S phase, just as the association of E2F with cyclin A became detectable. We characterized the cyclin E-E2F complex further to show that both the cyclin-dependent kinase-2 (cdk2) and p107 were present. Therefore, the p107/E2F complex is associated with two different cdk2 kinase complexes--one containing cyclin A and the other containing cyclin E--and the appearance of these complexes is temporally regulated during the cell cycle. The presence of cyclin E/E2F complexes in the G1 phase suggests a role for cyclin E in the control of genes required for the G1-to-S transition.

Purification of membranes and identification of phase-specific proteins of the dimorphic pathogenic fungus Histoplasma capsulatum

Plasma membrane vesicles from the yeast and mycelial phases of Histoplasma capsulatum have been purified and characterized. The method of purification involved differential centrifugation of ballistically fractured cells followed by sedimentation through discontinuous sucrose density gradient and equilibrium centrifugation. Purity of the preparation was assessed by electron microscopy. The protein composition of the membrane preparations from the yeast and mycelial phases of the fungus was analyzed by polyacrylamide gels. A comparison of the two morphologic phases revealed quantitative and qualitative differences in the expressions of several membrane-specific proteins. Physical differences in the appearance of the membranes were also observed by electron micrography of membrane preparations. Alteration in membrane fluidity may be one of the many causes for differences in the appearance of membrane vesicles in the two phases.

An autoradiographical study of amino acid and nucleoside incorporation during the cell cycle of Amoeba proteus.

The incorporation of tritiated thymidine, uridine and leucine, into the acid-precipitable material of DNA. RNA and proteins, respectively, was studied by autoradiography throughout the cell cycle of Amoeba proteus. DNA synthesis occupied the first 17 h of the cycle (57 h long) and 2 peaks between 0.5 and 9.13 h accounted for the majority of the thymidine incorporation. RNA synthesis was represented by a series of peak uridine grain counts, the 3 major peaks occurring at 10, 26-27 and 47-48 h. The incorporation of leucine also followed a pattern of peaks and dips, the main peaks occurring 1-2 h after the major increases in uridine incorporation. The fraction of label present over the nucleus decreased during the cell cycle, and this was probably due to a lowered incorporation of the leucine label by proteins synthesized in the cytoplasm and destined to become nuclear proteins. The incorporation patterns of 6 amino acids (arginine, aspartic acid, leucine, lysine, serine and valine) were studied individually during 3 periods of the cell cycle: 0-10 h (S phase); 20-30 h (early G2); and 40-50 h (mid-late G2). Variations in the intensity and timings of the incorporation maxima of the amino acids were observed, although the timings of increased grain counts of some of the amino acids frequently coincided. "Unique" incorporation peaks (i.e. only observed in one of the amino acids studied) possibly indicate the synthesis of phase-specific proteins. The amino acid and nucleoside incorporation profiles presented in this paper will enable the results obtained from future studies on amoebae to be related to the macromolecular synthesis patterns.

G2 phase-specific proteins of HeLa cells.

The objective of this study was to determine if HeLa cells irreversibly arrested in G2 phase of the cell cycle by a brief exposure to a nitrosourea compound were deficient in certain proteins when compared with G2-synchronized cells. Total cellular proteins of G2-synchronized, G2-arrested, and S phase-synchronized cells were compared by two-dimensional polyacrylamide gel electrophoresis. The S phase cells differed from the G2-synchronized and G2-arrested cells by the absence of about 35 and 25 protein spots, respectively, of a total of nearly 150. At least nine protein spots in the molecular weight range of 4--5 X 10(4) that were present in the G2-synchronized cells were absent in both the G2-arrested and the S phase cells. Thus, these studies suggest that the missing proteins are probably necessary for the transition of cells from G2 phase to mitosis. Supplying the missing proteins to the G2-arrested cells by fusion with G2-synchronized cells facilitated the entry of the former into mitosis.