Comparative genomics in <i>Chlamydomonas</i> and <i>Plasmodium</i> identifies an ancient nuclear envelope protein family essential for sexual reproduction in protists, fungi, plants, and vertebrates

Ning, Jue; Otto, Thomas D.; Pfander, Claudia; Schwach, Frank; Brochet, Mathieu; Bushell, Ellen; Goulding, David; Sanders, Mandy; Lefebvre, Paul; Pei, Jimin; Grishin, Nick V.; Vanderlaan, Gary; Billker, Oliver; Snell, William J.

doi:10.1101/gad.212746.112

Cited by 89 publications

(146 citation statements)

References 54 publications

Supporting

Mentioning

138

Contrasting

Order By: Relevance

“…A previous study of plus and minus gamete-specific genes focused on cell type genes whose expression was up-regulated during the process of mating (Ning et al, 2013). However, direct comparison with the previous data is confounded by differences in annotation between genome versions used to define transcripts as well as in the different clustering criteria used in the two studies.…”

Section: Discussionmentioning

confidence: 94%

“…While previous high-throughput expression studies have focused on the transcriptional programs underlying processes such as nutrient deprivation (Nguyen et al, 2008;González-Ballester et al, 2010;Toepel et al, 2011Toepel et al, , 2013Schmollinger et al, 2014), environmental responses (Simon et al, 2008(Simon et al, , 2013Matsuo et al, 2011;Fang et al, 2012), flagellar biogenesis (Albee et al, 2013), lipid accumulation Boyle et al, 2012;Lv et al, 2013), and diurnal rhythms (Idoine et al, 2014;Panchy et al, 2014), only a few studies have explored the genome-wide transcriptional and epigenetic changes associated with the sexual cycle (Kubo et al, 2008;Ning et al, 2013;Aoyama et al, 2014). Several genes expressed in the early zygote, termed EZY genes, have predicted functions related to cell wall production, vesicular transport, and secretion (Ferris and Goodenough, 1987;Ferris et al, 2002;Kubo et al, 2008).…”

mentioning

confidence: 99%

See 1 more Smart Citation

Dynamic changes in the transcriptome and methylome of Chlamydomonas reinhardtii throughout its life cycle

et al. 2015

View full text Add to dashboard Cite

; 0000-0001-9355-9564 (M.P.).The green alga Chlamydomonas reinhardtii undergoes gametogenesis and mating upon nitrogen starvation. While the steps involved in its sexual reproductive cycle have been extensively characterized, the genome-wide transcriptional and epigenetic changes underlying different life cycle stages have yet to be fully described. Here, we performed transcriptome and methylome sequencing to quantify expression and DNA methylation from vegetative and gametic cells of each mating type and from zygotes. We identified 361 gametic genes with mating type-specific expression patterns and 627 genes that are specifically induced in zygotes; furthermore, these sex-related gene sets were enriched for secretory pathway and alga-specific genes. We also examined the C. reinhardtii nuclear methylation map with base-level resolution at different life cycle stages. Despite having low global levels of nuclear methylation, we detected 23 hypermethylated loci in gene-poor, repeat-rich regions. We observed mating type-specific differences in chloroplast DNA methylation levels in plus versus minus mating type gametes followed by chloroplast DNA hypermethylation in zygotes. Lastly, we examined the expression of candidate DNA methyltransferases and found three, DMT1a, DMT1b, and DMT4, that are differentially expressed during the life cycle and are candidate DNA methylases. The expression and methylation data we present provide insight into cell type-specific transcriptional and epigenetic programs during key stages of the C. reinhardtii life cycle.Chlamydomonas reinhardtii is a unicellular, biflagellate species of green alga found primarily in fresh water and soil (Harris et al., 2009). C. reinhardtii is an important reference organism for diverse eukaryotic cellular and metabolic processes, including photosynthetic biology (Rochaix, 2001), flagellar function and biogenesis (Silflow and Lefebvre, 2001), nutrient homeostasis (Grossman, 2000;Merchant et al., 2006;Glaesener et al., 2013), and sexual cycles (Goodenough et al., 2007). The nuclear and chloroplast genomes of C. reinhardtii have been fully sequenced, enabling genomic and epigenomic analyses (Maul et al., 2002;Merchant et al., 2007). The approximately 112-Mb haploid C. reinhardtii nuclear genome comprises 17 chromosomes. The circular chloroplast DNA (cpDNA) genome is 203 kb and present in 80 to 100 copies per cell that are organized into eight to 10 nucleoprotein complexes called nucleoids, which are distributed through the stroma.Like many unicellular eukaryotes, C. reinhardtii has a biphasic life cycle where haploid cells can reproduce vegetatively by mitotic division or, alternatively, undergo a sexual cycle. Vegetative cells can propagate indefinitely when provided with nutrients and light. Upon nitrogen starvation, however, cells stop dividing and differentiate into gametes whose mating type (plus or minus) is determined genetically by an approximately 300-kb mating type locus on chromosome 6, with two haplotypes, MT+ and MT2 (Umen, 2011; De Hoff et al.,...

show abstract

Section: Discussionmentioning

confidence: 94%

mentioning

confidence: 99%

Dynamic changes in the transcriptome and methylome of Chlamydomonas reinhardtii throughout its life cycle

et al. 2015

View full text Add to dashboard Cite

show abstract

“…In addition, a transcript coding for a dynamin-like protein (Cre13g.569000.t1.1) was significantly upregulated. This protein is present in the same expression cluster as MIP1 in Ning et al (33); therefore, it might be involved in the CV cycle, possibly during systole.…”

Section: Osmoregulation Inmentioning

confidence: 87%

The Contractile Vacuole as a Key Regulator of Cellular Water Flow in Chlamydomonas reinhardtii

2014

View full text Add to dashboard Cite

Most freshwater flagellates use contractile vacuoles (CVs) to expel excess water. We have used Chlamydomonas reinhardtii as a green model system to investigate CV function during adaptation to osmotic changes in culture medium. We show that the contractile vacuole in Chlamydomonas is regulated in two different ways. The size of the contractile vacuoles increases during cell growth, with the contraction interval strongly depending on the osmotic strength of the medium. In contrast, there are only small fluctuations in cytosolic osmolarity and plasma membrane permeability. Modeling of the CV membrane permeability indicates that only a small osmotic gradient is necessary for water flux into the CV, which most likely is facilitated by the aquaporin major intrinsic protein 1 (MIP1). We show that MIP1 is localized to the contractile vacuole, and that the expression rate and protein level of MIP1 exhibit only minor fluctuations under different osmotic conditions. In contrast, SEC6, a protein of the exocyst complex that is required for the water expulsion step, and a dynamin-like protein are upregulated under strong hypotonic conditions. The overexpression of a CreMIP1-GFP construct did not change the physiology of the CV. The functional implications of these results are discussed. In hypotonic media, cells/organisms take up water by osmosis. Water uptake occurs only if the water potential inside the cell is more negative than that outside the cell. The amount of water taken up in a given time depends on (i) the water potential gradient between the medium and the cell interior, (ii) the surface area of the plasma membrane (PM), and (iii) the extent to which the PM is permeable to water. Cells can use three strategies to prevent bursting caused by the osmotic influx of water in a hypotonic environment. First, organisms can modify the composition of its interior, its surface area, and/or its PM permeability to limit water uptake. Second, organisms can use a cell wall to generate a cell wall pressure potential (turgor) to balance the osmotic water potential, as many algae, plants, and fungi do. However, many unicellular protists do not possess a rigid cell wall. Instead, these protists use a third strategy: they employ water pumps called contractile vacuoles (CVs) to remove excess water. CVs are specialized vacuoles that slowly accumulate water during diastole and periodically expel the liquid rapidly into the medium (systole) (1-4).Although CV morphologies and behaviors differ among various organisms (see for a recent comparison of the contractile vacuoles of a variety of protists), the basic mechanism (water uptake into the CV by osmosis) appears to be conserved between different eukaryotes. The same proteins/ cellular processes have been implicated in CV function in Amoeba, Dictyostelium, Paramecium, Trypanosoma, and green algae (e.g., proton pumps and aquaporins) (3, 4, 6). However, we still do not know anything about what other factors (ion transport systems) are needed to build up the necessary osmotic gradient in a...

show abstract

“…4A-C,E). To test whether the absence of the protein at the mating structure was a consequence of the low expression of the upper form of HAP2-ecto+TMD, we incubated the gametes with di-butyryl cAMP (db-cAMP), a treatment that leads to upregulation of HAP2 transcription and translation (Liu et al, 2010;Ning et al, 2013). Such activated cells still lacked HAP2-ecto+TMD at the mating structure, and the activated HAP2-ecto+TMD cells were incapable of fusion with plus gametes (Fig.…”

Section: Resultsmentioning

confidence: 99%

The cytoplasmic domain of the gamete membrane fusion protein HAP2 targets the protein to the fusion site in Chlamydomonas and regulates the fusion reaction

et al. 2015

Self Cite

View full text Add to dashboard Cite

Cell-cell fusion between gametes is a defining step during development of eukaryotes, yet we know little about the cellular and molecular mechanisms of the gamete membrane fusion reaction. HAP2 is the sole gamete-specific protein in any system that is broadly conserved and shown by gene disruption to be essential for gamete fusion. The wide evolutionary distribution of HAP2 (also known as GCS1) indicates it was present in the last eukaryotic common ancestor and, therefore, dissecting its molecular properties should provide new insights into fundamental features of fertilization. HAP2 acts at a step after membrane adhesion, presumably directly in the merger of the lipid bilayers. Here, we use the unicellular alga Chlamydomonas to characterize contributions of key regions of HAP2 to protein location and function. We report that mutation of three strongly conserved residues in the ectodomain has no effect on targeting or fusion, although short deletions that include those residues block surface expression and fusion. Furthermore, HAP2 lacking a 237-residue segment of the cytoplasmic region is expressed at the cell surface, but fails to localize at the apical membrane patch specialized for fusion and fails to rescue fusion. Finally, we provide evidence that the ancient HAP2 contained a juxta-membrane, multicysteine motif in its cytoplasmic region, and that mutation of a cysteine dyad in this motif preserves protein localization, but substantially impairs HAP2 fusion activity. Thus, the ectodomain of HAP2 is essential for its surface expression, and the cytoplasmic region targets HAP2 to the site of fusion and regulates the fusion reaction.

show abstract

Comparative genomics in Chlamydomonas and Plasmodium identifies an ancient nuclear envelope protein family essential for sexual reproduction in protists, fungi, plants, and vertebrates

Cited by 89 publications

References 54 publications

Dynamic changes in the transcriptome and methylome of Chlamydomonas reinhardtii throughout its life cycle

Dynamic changes in the transcriptome and methylome of Chlamydomonas reinhardtii throughout its life cycle

The Contractile Vacuole as a Key Regulator of Cellular Water Flow in Chlamydomonas reinhardtii

The cytoplasmic domain of the gamete membrane fusion protein HAP2 targets the protein to the fusion site in Chlamydomonas and regulates the fusion reaction

Contact Info

Product

Resources

About