New Insights into the Role of the Maize Ameiotic1 Locus

In maize the am1-1 mutant allele results in both the male and female meiocytes undergoing mitosis in place of the meiotic divisions. A second mutant allele am1-praI enables both the male and female meiocytes to proceed to the early zygotene stage of meiotic prophase I before being blocked. Here we report on three new alleles that allow all male meiocytes to undergo mitosis but in female meiocytes approximately one quarter (am1-2), one half (am1-485), or all (am1-489) of them are blocked at an abnormal interphase stage. Previous analysis has shown that am1-praI is dominant to am1-1 in male meiocytes. Cytological analysis of heteroallelic combinations in female meiocytes now indicates a dominance relationship of am1-praI > am1-1 > am1-2/am1-485 > am1-489. The evidence provided by the female phenotypes of the new mutant alleles suggest that, whereas the normal am1 allele is required for the meiocytes to proceed through meiosis, a partially functional allele may be required for their diversion into a mitotic division. The partial or complete blockage of mitosis in female meiocytes carrying the new am1 alleles rules out the possibility that the mitotic division of mutant meiocytes reflects a simple default pathway for cells that cannot initiate meiosis. This locus may have a dual function.     

Insights into Maize LEA proteins: from proteomics to functional approaches

LEA (late embryogenesis abundant) proteins participate in plant stress tolerance responses, but the mechanisms by which protection occurs are not fully understood. In the present work the unfolded proteins from maize dry embryos were analyzed by mass spectrometry. Twenty embryo proteins were identified, and among them 13 corresponded to LEA-type proteins. We selected three major LEA proteins, Emb564, Rab17 and Mlg3, belonging to groups 1, 2 and 3, respectively, and we undertook a comparative study in order to highlight differences among them. The post-translational modifications of native proteins were analyzed and the anti-aggregation properties of recombinant Emb564, Rab17 and Mgl3 proteins were evaluated in vitro. In addition, the protective effects of the LEA proteins were assessed in living cells under stress in Escherichia coli cells and in Nicotiana bentamiana leaves agroinfiltrated with fluorescent LEA-green fluorescent protein (GFP) fusions. Protein visualization by confocal microscopy indicated that cells expressing Mg3-GFP showed reduced cell shrinkage effects during dehydration and that Rab17-GFP co-localized to leaf oil bodies after heat shock. Overall, the results highlight differences and suggest functional diversity among maize LEA groups.     

Insights into the Effects of Long-Term Artificial Selection on Seed Size in Maize

Grain produced from cereal crops is a primary source of human food and animal feed worldwide. To understand the genetic basis of seed-size variation, a grain yield component, we conducted a genome-wide scan to detect evidence of selection in the maize Krug Yellow Dent long-term divergent seed-size selection experiment. Previous studies have documented significant phenotypic divergence between the populations. Allele frequency estimates for ∼3 million single nucleotide polymorphisms (SNPs) in the base population and selected populations were estimated from pooled whole-genome resequencing of 48 individuals per population. Using F_ST values across sliding windows, 94 divergent regions with a median of six genes per region were identified. Additionally, 2729 SNPs that reached fixation in both selected populations with opposing fixed alleles were identified, many of which clustered in two regions of the genome. Copy-number variation was highly prevalent between the selected populations, with 532 total regions identified on the basis of read-depth variation and comparative genome hybridization. Regions important for seed weight in natural variation were identified in the maize nested association mapping population. However, the number of regions that overlapped with the long-term selection experiment did not exceed that expected by chance, possibly indicating unique sources of variation between the two populations. The results of this study provide insights into the genetic elements underlying seed-size variation in maize and could also have applications for other cereal crops.     

Insights into the kinetochore

The Ndc80 complex is a core component of the kinetochore, which links chromosomes to microtubules. Recently, Ciferri et al. (2008) published an atomic-level structure of the complex with implications for kinetochore architecture and for the generation and control of chromosome movements during mitosis.     

Comparative Proteomic Analyses Provide New Insights into Low Phosphorus Stress Responses in Maize Leaves

Phosphorus deficiency limits plant growth and development. To better understand the mechanisms behind how maize responds to phosphate stress, we compared the proteome analysis results of two groups of maize leaves that were treated separately with 1,000 µM (control, +P) and 5 µM of KH₂PO₄ (intervention group, −P) for 25 days. In total, 1,342 protein spots were detected on 2-DE maps and 15.43% had changed (P<0.05; ≥1.5-fold) significantly in quantity between the +P and −P groups. These proteins are involved in several major metabolic pathways, including photosynthesis, carbohydrate metabolism, energy metabolism, secondary metabolism, signal transduction, protein synthesis, cell rescue and cell defense and virulence. The results showed that the reduction in photosynthesis under low phosphorus treatment was due to the down-regulation of the proteins involved in CO₂ enrichment, the Calvin cycle and the electron transport system. Electron transport and photosynthesis restrictions resulted in a large accumulation of peroxides. Maize has developed many different reactive oxygen species (ROS) scavenging mechanisms to cope with low phosphorus stress, including up-regulating its antioxidant content and antioxidase activity. After being subjected to phosphorus stress over a long period, maize may increase its internal phosphorus utilization efficiency by altering photorespiration, starch synthesis and lipid composition. These results provide important information about how maize responds to low phosphorus stress.     

Insights into prion biology

Protein misfolding and assembly into ordered, self-templating aggregates (amyloid) has emerged as a novel mechanism for regulating protein function. For a subclass of amyloidogenic proteins known as prions, this process induces transmissible changes in normal cellular physiology, ranging from neurodegenerative disease in animals and humans to new traits in fungi. The severity and stability of these altered phenotypic states can be attenuated by the conformation or amino-acid sequence of the prion, but in most of these cases, the protein retains the ability to form amyloid in vitro. Thus, our ability to link amyloid formation in vitro with its biological consequences in vivo remains a challenge. In two recent studies, we have begun to address this disconnect by assessing the effects of the cellular environment on traits associated with the misfolding of the yeast prion Sup35. Remarkably, the effects of quality control pathways and of limitations on protein transfer in vivo amplify the effects of even slight differences in the efficiency of Sup35 misfolding, leading to dramatic changes in the associated phenotype. Together, our studies suggest that the interplay between protein misfolding pathways and their cellular context is a crucial contributor to prion biology.     

Insights into Conifer Giga-Genomes

Insights from sequenced genomes of major land plant lineages have advanced research in almost every aspect of plant biology. Until recently, however, assembled genome sequences of gymnosperms have been missing from this picture. Conifers of the pine family (Pinaceae) are a group of gymnosperms that dominate large parts of the world’s forests. Despite their ecological and economic importance, conifers seemed long out of reach for complete genome sequencing, due in part to their enormous genome size (20–30 Gb) and the highly repetitive nature of their genomes. Technological advances in genome sequencing and assembly enabled the recent publication of three conifer genomes: white spruce (Picea glauca), Norway spruce (Picea abies), and loblolly pine (Pinus taeda). These genome sequences revealed distinctive features compared with other plant genomes and may represent a window into the past of seed plant genomes. This Update highlights recent advances, remaining challenges, and opportunities in light of the publication of the first conifer and gymnosperm genomes.Conifers are the most widely distributed group of gymnosperms, with 600 to 630 species in 69 genera, including 220 to 250 species of the Pinaceae family (Wang and Ran, 2014). Coniferous forests cover an estimated 39% of the world’s forests (Armenise et al., 2012). Conifers dominate many natural and planted forests in the northern hemisphere and are also planted as exotics for commercial forestry in the southern hemisphere. The importance of conifers for global ecosystem services, their value for forestry-dependent economies, and their contrasting biology with angiosperms are major drivers behind efforts to understand the complex structure, functions, and evolution of their genomes. However, owing to their nonmodel system attributes (i.e. slow-growing and long-lived life history traits), extremely large genome size (Fig. 1), and repeat-rich genome sequence with repeats mostly in the form of transposable elements, no reports of a conifer genome assembly, or any gymnosperm genome for that matter (Soltis and Soltis, 2013), were published until recently. Following early releases of the white spruce (Picea glauca) and loblolly pine (Pinus taeda) genome sequences in public databases (e.g. National Center for Biotechnology Information and http://dendrome.ucdavis.edu/treegenes/), a series of articles described the first conifer genome assemblies for Norway spruce (Picea abies; Nystedt et al., 2013) and interior white spruce, a genetic admix of white spruce (Birol et al., 2013) and loblolly pine (Neale et al., 2014; Zimin et al., 2014). Norway spruce is a prominent forest tree in northern Europe. White spruce is a dominant tree species across the large Canadian forest landscape. Loblolly pine dominates commercial forestry in the southeastern United States. White spruce, Norway spruce, and loblolly pine represent some of the most economically important conifers worldwide, and they are the subjects of important tree improvement/breeding programs (Mullin et al., 2011). This Update highlights significant insights obtained from these genomes as well as some ongoing challenges and recent developments in conifer genomics.Open in a separate windowFigure 1.Size and assembly of conifer genomes compared with other plant genomes. Genome size is plotted against the number of scaffolds divided by the haploid chromosome number for a range of plant species. As such, an assembly that reconstructs a genome with perfect contiguity will have a value of 1, and values greater than 1 represent increasing genome fragmentation. Genome assemblies that utilized Sanger sequencing either in full or in part are represented as white circles. Assemblies constructed using only next generation sequencing technologies are represented as black circles. Both axes are plotted on a log₁₀ scale. With the exception of Populus tremula, Hordeum vulgare, and the three conifer genomes, all genomes were obtained from the Phytozome resource (version 10; http://phytozome.jgi.doe.gov/). The early release draft assembly of P. tremula was obtained from the PopGenIE.org FTP resource (ftp://popgenie.org/popgenie/UPSC_genomes/UPSC_Draft_Assemblies/Current/Genome/) and H. vulgare ‘Morex’ from the Munich Information Center for Protein Sequences barley genome database FTP resource (ftp://ftpmips.helmholtz-muenchen.de/plants/barley/public_data/sequences/). The conifer genomes are detailed by Birol et al. (2013), Nystedt et al. (2013), and Zimin et al. (2014).     

Genomic Insights into Bifidobacteria

Summary: Since the discovery in 1899 of bifidobacteria as numerically dominant microbes in the feces of breast-fed infants, there have been numerous studies addressing their role in modulating gut microflora as well as their other potential health benefits. Because of this, they are frequently incorporated into foods as probiotic cultures. An understanding of their full interactions with intestinal microbes and the host is needed to scientifically validate any health benefits they may afford. Recently, the genome sequences of nine strains representing four species of Bifidobacterium became available. A comparative genome analysis of these genomes reveals a likely efficient capacity to adapt to their habitats, with B. longum subsp. infantis exhibiting more genomic potential to utilize human milk oligosaccharides, consistent with its habitat in the infant gut. Conversely, B. longum subsp. longum exhibits a higher genomic potential for utilization of plant-derived complex carbohydrates and polyols, consistent with its habitat in an adult gut. An intriguing observation is the loss of much of this genome potential when strains are adapted to pure culture environments, as highlighted by the genomes of B. animalis subsp. lactis strains, which exhibit the least potential for a gut habitat and are believed to have evolved from the B. animalis species during adaptation to dairy fermentation environments.     

Insights into eisosome assembly and organization

Eisosomes, large protein complexes that are predominantly composed of BAR-domain-containing proteins Pil1 and its homologs, are situated under the plasma membrane of ascomycetes. A successful targeting of Pil1 onto the future site of eisosome accompanies maturation of eisosome. During or after recruitment, Pil1 undergoes self-assembly into filaments that can serve as scaffolds to induce membrane furrows or invaginations. Although a consequence of the invagination is likely to redistribute particular proteins and lipids to a different location, the precise physiological role of membrane invagination and eisosome assembly awaits further investigation. The present review summarizes recent research findings within the field regarding the detailed structural and functional significance of Pil1 on eisosome organization.     

Insights into prion strains and neurotoxicity

Transmissible spongiform encephalopathies (TSEs) are neurodegenerative diseases that are caused by prions and affect humans and many animal species. It is now widely accepted that the infectious agent that causes TSEs is PrP(Sc), an aggregated moiety of the host-derived membrane glycolipoprotein PrP(C). Although PrP(C) is encoded by the host genome, prions themselves encipher many phenotypic TSE variants, known as prion strains. Prion strains are TSE isolates that, after inoculation into distinct hosts, cause disease with consistent characteristics, such as incubation period, distinct patterns of PrP(Sc) distribution and spongiosis and relative severity of the spongiform changes in the brain. The existence of such strains poses a fascinating challenge to prion research.     

Insights into the obligate methanotroph Methylococcus capsulatus

Completion of the genome sequence of Methylococcus capsulatus Bath is an important event in molecular microbiology, and an achievement for which the authors deserve congratulation. M. capsulatus, along with other methanotrophs, has been the subject of intense biochemical and molecular study because of its role in the global carbon cycle: the conversion of biogenic methane to carbon dioxide. The methane monooxygenase enzymes that are central to this process also have high biotechnological potential. Analysis of the genome sequence will potentially accelerate elucidation of the regulation of methane-dependent metabolism in obligate methanotrophs, and help explain the cause of obligate methanotrophy, the phenomenon making most methanotrophs unable to grow on any substrates other than methane and a very small number of other one-carbon compounds.     

Insights into the Functional Architecture of the Catalytic Center of a Maize β-Glucosidase Zm-p60.1

The maize (Zea mays) beta-glucosidase Zm-p60.1 has been implicated in regulation of plant development by the targeted release of free cytokinins from cytokinin-O-glucosides, their inactive storage forms. The crystal structure of the wild-type enzyme was solved at 2.05-A resolution, allowing molecular docking analysis to be conducted. This indicated that the enzyme specificity toward substrates with aryl aglycones is determined by aglycone aromatic system stacking with W373, and interactions with edges of F193, F200, and F461 located opposite W373 in a slot-like aglycone-binding site. These aglycone-active site interactions recently were hypothesized to determine substrate specificity in inactive enzyme substrate complexes of ZM-Glu1, an allozyme of Zm-p60.1. Here, we test this hypothesis by kinetic analysis of F193I/Y/W mutants. The decreased K(m) of all mutants confirmed the involvement of F193 in determining enzyme affinity toward substrates with an aromatic aglycone. It was unexpected that a 30-fold decrease in k(cat) was found in F193I mutant compared with the wild type. Kinetic analysis and computer modeling demonstrated that the F193-aglycone-W373 interaction not only contributes to aglycone recognition as hypothesized previously but also codetermines catalytic rate by fixing the glucosidic bond in an orientation favorable for attack by the catalytic pair, E186 and E401. The catalytic pair, assigned initially by their location in the structure, was confirmed by kinetic analysis of E186D/Q and E401D/Q mutants. It was unexpected that the E401D as well as C205S and C211S mutations dramatically impaired the assembly of a catalysis-competent homodimer, suggesting novel links between the active site structure and dimer formation.