International conference on “Photosynthesis research for sustainability-2013: in honor of Jalal A. Aliyev”, held during June 5–9, 2013, Baku, Azerbaijan

In this brief report, we provide a pictorial essay on an international conference “Photosynthesis Research for Sustainability-2013 in honor of Jalal A. Aliyev” that was held in Baku, Azerbaijan, during June 5–9, 2013 (http://photosynthesis2013.cellreg.org/). We begin this report with a brief note on Jalal Aliyev, the honored scientist, and on John Walker (1997 Nobel laureate in Chemistry) who was a distinguished guest and lecturer at the Conference. We briefly describe the Conference, and the program. In addition to the excellent scientific program, a special feature of the Conference was the presentation of awards to nine outstanding young investigators; they are recognized in this report. We have also included several photographs to show the pleasant ambience at this conference. (See http://photosynthesis2013.cellreg.org/Photo-Gallery.php; https://www.dropbox.com/sh/qcr124dajwffwh6/TlcHBvFu4H?m; and https://www.copy.com/s/UDlxb9fgFXG9/Baku for more photographs taken by the authors as well as by others.) We invite the readers to the next conferences on “Photosynthesis Research for Sustainability—2014: in honor of Vladimir A. Shuvalov” to be held during June 2–7, 2014, in Pushchino, Russia. Detailed information for this will be posted at the Website: http://photosynthesis2014.cellreg.org/, and for the subsequent conference on “Photosynthesis Research for Sustainability—2015” to be held in May or June 2015, in Baku, Azerbaijan, at http://photosynthesis2015.cellreg.org/.     

A novel deconvolution method for modeling UDP-N-acetyl-D-glucosamine biosynthetic pathways based on 13C mass isotopologue profiles under non-steady-state conditions

This article is a response to Wang and Luo. See correspondence article http://www.biomedcentral.com/1741-7007/10/30/ [WEBCITE] and the original research article http://www.biomedcentral.com/1741-7007/9/24 [WEBCITE].     

Aquatic vascular plants in Japanese lakes

This data paper describes the native vascular aquatic plant floras of 268 Japanese lakes recorded from 1899–2011. The data were compiled from 201 literature sources, most of which were written in Japanese and published in local journals or individual reports rather than in major scientific journals. The literature was searched using web-based services (i.e., Google Scholar, http://scholar.google.com/; CiNii, http://ci.nii.ac.jp/en; JDreamII, http://pr.jst.go.jp/jdream2/; and ISI, http://apps.webofknowledge.com) and by private communication with experts or local governments. Scientific names were consolidated under currently-accepted nomenclature. Four datasets, FloraDB, LakeDB, SpeciesDB, and LiteratureDB, were created to include records of the flora of each lake in each year, the names and locations of the lakes, the scientific names and synonyms of the aquatic vascular plants, and a literature list, respectively. These data can be used to study long-term changes in the species composition and/or richness of aquatic plants in Japanese lakes.     

Whole genome transcriptome polymorphisms in Arabidopsis thaliana

ArrayPlex is a software package that centrally provides a large number of flexible toolsets useful for functional genomics, including microarray data storage, quality assessments, data visualization, gene annotation retrieval, statistical tests, genomic sequence retrieval and motif analysis. It uses a client-server architecture based on open source components, provides graphical, command-line, and programmatic access to all needed resources, and is extensible by virtue of a documented application programming interface. ArrayPlex is available at http://sourceforge.net/projects/arrayplex/.     

A Novel Cholinergic Action of Alcohol and the Development of Tolerance to That Effect in Caenorhabditis elegans

The Prp43 DExD/H-box protein is required for progression of the biochemically distinct pre-messenger RNA and ribosomal RNA (rRNA) maturation pathways. In Saccharomyces cerevisiae, the Spp382/Ntr1, Sqs1/Pfa1, and Pxr1/Gno1 proteins are implicated as cofactors necessary for Prp43 helicase activation during spliceosome dissociation (Spp382) and rRNA processing (Sqs1 and Pxr1). While otherwise dissimilar in primary sequence, these Prp43-binding proteins each contain a short glycine-rich G-patch motif required for function and thought to act in protein or nucleic acid recognition. Here yeast two-hybrid, domain-swap, and site-directed mutagenesis approaches are used to investigate G-patch domain activity and portability. Our results reveal that the Spp382, Sqs1, and Pxr1 G-patches differ in Prp43 two-hybrid response and in the ability to reconstitute the Spp382 and Pxr1 RNA processing factors. G-patch protein reconstitution did not correlate with the apparent strength of the Prp43 two-hybrid response, suggesting that this domain has function beyond that of a Prp43 tether. Indeed, while critical for Pxr1 activity, the Pxr1 G-patch appears to contribute little to the yeast two-hybrid interaction. Conversely, deletion of the primary Prp43 binding site within Pxr1 (amino acids 102–149) does not impede rRNA processing but affects small nucleolar RNA (snoRNA) biogenesis, resulting in the accumulation of slightly extended forms of select snoRNAs, a phenotype unexpectedly shared by the prp43 loss-of-function mutant. These and related observations reveal differences in how the Spp382, Sqs1, and Pxr1 proteins interact with Prp43 and provide evidence linking G-patch identity with pathway-specific DExD/H-box helicase activity.     

Telomerase Recruitment in Saccharomyces cerevisiae Is Not Dependent on Tel1-Mediated Phosphorylation of Cdc13

In Saccharomyces cerevisiae, association between the Est1 telomerase subunit and the telomere-binding protein Cdc13 is essential for telomerase to be recruited to its site of action. A current model proposes that Tel1 binding to telomeres marks them for elongation, as the result of phosphorylation of a proposed S/TQ cluster in the telomerase recruitment domain of Cdc13. However, three observations presented here argue against one key aspect of this model. First, the pattern of Cdc13 phosphatase-sensitive isoforms is not altered by loss of Tel1 function or by mutations introduced into two conserved serines (S249 and S255) in the Cdc13 recruitment domain. Second, an interaction between Cdc13 and Est1, as monitored by a two-hybrid assay, is dependent on S255 but Tel1-independent. Finally, a derivative of Cdc13, cdc13–(S/TQ)₁₁→(S/TA)₁₁, in which every potential consensus phosphorylation site for Tel1 has been eliminated, confers nearly wild-type telomere length. These results are inconsistent with a model in which the Cdc13–Est1 interaction is regulated by Tel1-mediated phosphorylation of the Cdc13 telomerase recruitment domain. We propose an alternative model for the role of Tel1 in telomere homeostasis, which is based on the assumption that Tel1 performs the same molecular task at double-strand breaks (DSBs) and chromosome termini.TELOMERE length homeostasis is a highly regulated process that must balance telomere loss (as the result of incomplete replication and/or nucleolytic degradation) with telomeric repeat addition (through the action of telomerase and/or recombination). In the budding yeast Saccharomyces cerevisiae, a key regulatory event is recruitment of telomerase to chromosome ends by the telomere end-binding protein Cdc13 (Nugent et al. 1996; Evans and Lundblad 1999; Pennock et al. 2001; Bianchi et al. 2004; Chan et al. 2008). Recruitment relies on a direct interaction between Cdc13 and the Est1 subunit of telomerase (Pennock et al. 2001), which brings the catalytic core of the enzyme to its site of action. Disruption of this interaction, due to mutations in either CDC13 (cdc13-2) or EST1 (est1-60), results in an Est (ever-shorter-telomere) phenotype, as manifested by progressive telomere shortening and an eventual senescence phenotype. The recruitment activity of Cdc13, which resides in a 15-kDa N-terminal domain (Pennock et al. 2001), is sufficient to direct telomerase even to nontelomeric sites (Bianchi et al. 2004). As predicted by the recruitment model, association of telomerase with telomeres is greatly reduced in strains expressing the recruitment-defective cdc13-2 allele (Chan et al. 2008).Telomerase action at individual telomeres is highly regulated. Using an assay that monitors telomere addition at single nucleotide resolution (single telomere extension, STEX), Lingner and colleagues showed that only ∼7% of telomeres with wild-type (i.e., 300 bp) length are elongated by telomerase during a single cell cycle (Teixeira et al. 2004). However, as telomere length declines, the extension frequency increases: ∼20% of telomeres 200 bp in length and >40% of 100-bp-long telomeres are elongated (Teixeira et al. 2004; Arneric and Lingner 2007). The mechanism by which telomerase distinguishes short from long telomeres has been the subject of intense investigation. Work from a number of laboratories has led to the proposal that Tel1-dependent phosphorylation of Cdc13 at underelongated telomeres mediates the interaction between Cdc13 and the telomerase-associated Est1 protein, thus ensuring that telomerase is directed to the shortest telomeres in a population. In support of this model, the Est1 and Est2 telomerase subunits exhibit enhanced association with telomeres that have been artificially shortened, whereas Cdc13 displays length-independent association with telomeres (Bianchi and Shore 2007; Sabourin et al. 2007). This suggests that the preferential elongation of shorter telomeres is controlled at the level of recruitment of the telomerase holoenzyme by Cdc13. Furthermore, efficient association of Est1 and Est2 with chromosome ends requires Tel1 and Mre11 (which acts in the same pathway as Tel1 for telomere length regulation; Nugent et al. 1998; Ritchie and Petes 2000) but not Mec1 (Takata et al. 2005; Goudsouzian et al. 2006). Tel1 itself is also telomere bound (Takata et al. 2004), with enhanced binding to shorter telomeres (Bianchi and Shore 2007; Hector et al. 2007; Sabourin et al. 2007; Abdallah et al. 2009), although there is considerable controversy over the degree and timing of Tel1 association with chromosome termini during the cell cycle. As expected for a key regulator of the interaction between Cdc13 and a telomerase subunit, a tel1-Δ strain has short telomeres (Lustig and Petes 1986), although telomere length is not impaired enough to confer the Est phenotype displayed by cdc13-2 and est1-60 strains.Implicit in the above proposal is that Cdc13 must be a direct substrate of Tel1. In support of this, Teng and colleagues reported several years ago that the recruitment domain of Cdc13 has a cluster of potential Tel1 (and/or Mec1) phosphorylation sites (Tseng et al. 2006). Substrates of the DNA damage kinases often contain several closely spaced phosphorylation sites, termed S/TQ cluster domains (SCDs), which are considered a structural hallmark of many DNA damage-response proteins (Traven and Heierhorst 2005). On the basis of in vitro kinase assays with GST fusions to 75- to 90-amino-acid portions of the Cdc13 recruitment domain, Tseng et al. 2006 concluded that four SQ sites in the recruitment domain of Cdc13 are overlapping substrates for both Tel1 and Mec1, leading to the proposal that telomerase recruitment in S. cerevisiae is regulated by Tel1-dependent phosphorylation of Cdc13.The above model makes a key prediction: in a tel1-Δ strain, telomerase should no longer exhibit a length-dependent pattern of elongation. However, preferential elongation of short telomeres still occurs at native chromosome ends in the absence of Tel1 (Arneric and Lingner 2007). In addition, Petes and colleagues have argued, on the basis of epistasis data, that Tel1 performs an indirect role in the telomerase pathway, rather than directly targeting a telomerase regulator (Ritchie et al. 1999; Ritchie and Petes 2000). These observations are not easily explained, if preferential recognition of short telomeres by telomerase is mediated by Tel1-dependent phosphorylation of Cdc13. In this current study, we have re-examined the evidence for phosphorylation of Cdc13 as a regulatory mechanism for telomere length homeostasis. We report on a series of observations that indicate that Tel1 contributes to telomere length control through a mechanism other than phosphorylation of the Cdc13 S/TQ cluster.     

c-Type Cytochrome Assembly in Saccharomyces cerevisiae: A Key Residue for Apocytochrome c1/Lyase Interaction

The electron transport chains in the membranes of bacteria and organelles generate proton-motive force essential for ATP production. The c-type cytochromes, defined by the covalent attachment of heme to a CXXCH motif, are key electron carriers in these energy-transducing membranes. In mitochondria, cytochromes c and c₁ are assembled by the cytochrome c heme lyases (CCHL and CC₁HL) and by Cyc2p, a putative redox protein. A cytochrome c₁ mutant with a CAPCH heme-binding site instead of the wild-type CAACH is strictly dependent upon Cyc2p for assembly. In this context, we found that overexpression of CC₁HL, as well as mutations of the proline in the CAPCH site to H, L, S, or T residues, can bypass the absence of Cyc2p. The P mutation was postulated to shift the CXXCH motif to an oxidized form, which must be reduced in a Cyc2p-dependent reaction before heme ligation. However, measurement of the redox midpoint potential of apocytochrome c₁ indicates that neither the P nor the T residues impact the thermodynamic propensity of the CXXCH motif to occur in a disulfide vs. dithiol form. We show instead that the identity of the second intervening residue in the CXXCH motif is key in determining the CCHL-dependent vs. CC₁HL-dependent assembly of holocytochrome c₁. We also provide evidence that Cyc2p is dedicated to the CCHL pathway and is not required for the CC₁HL-dependent assembly of cytochrome c₁.THE c-type cytochromes, also referred to as cytochrome c, represent a universal class of heme-containing proteins that function as electron carriers in the energy-transducing pathways of bacteria, plastids, and mitochondria (Thöny-Meyer 1997; Nakamoto et al. 2000; Bonnard et al. 2010). Because cytochromes c carry a heme covalently attached to a CXXCH motif, they constitute an attractive object of study to address the question of cofactor protein assembly. The biochemical requirements for cytochrome c assembly were deduced from in vivo and in vitro studies, and the conclusion is that both apocytochromes c and heme are transported independently across at least one biological membrane and maintained as reduced prior to catalysis of the heme attachment reaction (Allen et al. 2003; Hamel et al. 2009; Kranz et al. 2009; Sanders et al. 2010). Bacterial cytochromes c are assembled in the periplasmic space, a compartment where cysteine pairs in proteins form disulfide bonds in reactions catalyzed by dedicated enzymes (Inaba 2009; Kadokura and Beckwith 2010). The current thinking holds that a c-type apocytochrome is a substrate of the disulfide bond-forming pathway, which introduces an intramolecular disulfide between the two cysteines of the CXXCH sequence (Allen et al. 2003; Sanders et al. 2010). This disulfide needs to be reduced to a dithiol to provide free sulfhydryls for the heme ligation. Consistent with this view is the fact that groups of specific oxido-reductases that constitute a transmembrane dithiol-disulfide relay from the cytosol to the periplasmic space have been shown to function as c-type cytochrome assembly factors (Allen et al. 2003; Kadokura et al. 2003; Mapller and Hederstedt 2006; Sanders et al. 2010). The proposal that the components of this pathway control the in vivo redox status of the CXXCH sulfhydryls has been inferred from the presence of motifs in their protein sequences that are consistent with a function in redox chemistry and also from the demonstration that their recombinant forms participate in dithiol–disulfide exchange reactions (Monika et al. 1997; Setterdahl et al. 2000). Moreover, the ability of exogenous thiol compounds to bypass the lack of these factors in vivo substantiates the view that the redox components have a disulfide-reducing activity in the pathway (e.g., Sambongi and Ferguson 1994; Fabianek et al. 1998; Beckett et al. 2000; Deshmukh et al. 2000; Bardischewsky and Friedrich 2001; Erlendsson and Hederstedt 2002; Erlendsson et al. 2003; Feissner et al. 2005; Turkarslan et al. 2008).While the role of these pathways is well established in bacteria, much less is known about the components that catalyze thiol/disulfide chemistry in the mitochondrial intermembrane space (IMS), which is topologically equivalent to the bacterial periplasm. By analogy with the bacterial pathways, the participation of redox-active factors that catalyze thiol formation is expected, as the mitochondrial IMS houses two c-type cytochromes, the soluble cytochrome c and the membrane-bound cytochrome c₁, both of which function in respiration. In fungi, heme attachment to apocytochromes c and c₁ is dependent upon the IMS resident cytochrome c and c₁ heme lyases, CCHL and CC₁HL, although the exact role of these lyases in the assembly process is still unclear (Dumont et al. 1987; Zollner et al. 1992). Conversion of apocytochrome to holocytochrome c depends only on CCHL, while apocytochrome c₁ can be acted upon by both CCHL and CC₁HL (Matner and Sherman 1982; Dumont et al. 1987; Stuart et al. 1990; Zollner et al. 1992; Bernard et al. 2003). In animals, apoforms of cytochromes c and c₁ are assembled by a unique heme lyase, HCCS, which carries both the CCHL and CC₁HL activities (Prakash et al. 2002; Schwarz and Cox 2002; Bernard et al. 2003).Cyc2p, a component first described as a mitochondrial biogenesis factor in yeast (Matner and Sherman 1982; Dumont et al. 1993; Pearce et al. 1998; Sanchez et al. 2001), was recently rediscovered in the context of cytochrome c₁ maturation (Bernard et al. 2003). Cyc2p is located at the mitochondrial inner membrane with its C-terminal domain containing a non-covalently bound FAD exposed to the IMS (Bernard et al. 2005). A redox function for Cyc2p is likely based on the finding that a recombinant form of the molecule exhibits a NAD(P)H-dependent reductase activity (Bernard et al. 2005). However, as Cyc2p activity is not essential for the maturation process, a functional redundancy was postulated based on the fact that a cyc2-null mutant still assembles holoforms of cytochromes c and c₁ (Bernard et al. 2005). The absolute requirement of Cyc2p was revealed via genetic analysis of the cyc2-null cyt1-34 combination that displays a synthetic respiratory-deficient phenotype with loss of holocytochrome c₁ assembly (Bernard et al. 2005). The cyt1-34 mutation maps to the gene encoding cytochrome c₁ and results in a CAPCH heme-binding site replacing the wild-type CAACH site (Bernard et al. 2005). The synthetic interaction is specific for the cyt1-34 allele carrying the A-to-P mutation and is not observed in a cyc2-null cyt1-48 strain carrying an A-to-D mutation at the heme-binding site of apocytochrome c₁ (Bernard et al. 2005). The fact that Cyc2p becomes essential when the cytochrome c₁ heme-binding site carries an A-to-P mutation suggests that the CXXCH motif could be the target of Cyc2p action in vivo. One possible interpretation for this observation is that the P residue alters the reactivity of the cysteinyl thiols to redox chemistry so that the apocytochrome c₁ CAPCH heme-binding site occurs in an oxidized (disulfide) form, which must be reduced in a Cyc2p-dependent reaction before heme attachment can occur.In this article, we have undertaken a genetic approach to elucidate this pathway and searched for suppressors that alleviate the respiratory deficiency of the cyc2-null cyt1-34 strain. Either overexpression of CC₁HL or replacement of the P mutation in the heme-binding site by H, L, S, or T residues restore the assembly of holocytochrome c₁. In vitro measurement of redox potential of apoforms of CA(A/P/T)CH cytochrome c₁ indicates that there is no change in the thermodynamic stability of the disulfide at the CXXCH motif that could account for the Cyc2p-dependent assembly of cytochrome c₁. Genetic studies reveal that the replacement of the second A residue at the CAACH motif by H, L, P, S, and T residues is key in determining the conversion of apocytochrome c₁ to its corresponding holoform via the CCHL and/or CC₁HL-dependent pathway. We also demonstrate that Cyc2p is a component dedicated to the CCHL pathway and is not required for the CC₁HL-dependent assembly of cytochrome c₁. We propose that the CAPCH cytochrome c₁ is strictly dependent upon CCHL and Cyc2p for its assembly but becomes a substrate of CC₁HL upon overexpression of CC₁HL or in the presence of H, L, S, or T mutations.     

Remodeling of the Rad51 DNA Strand-Exchange Protein by the Srs2 Helicase

Homologous recombination is associated with the dynamic assembly and disassembly of DNA–protein complexes. Assembly of a nucleoprotein filament comprising ssDNA and the RecA homolog, Rad51, is a key step required for homology search during recombination. The budding yeast Srs2 DNA translocase is known to dismantle Rad51 filament in vitro. However, there is limited evidence to support the dismantling activity of Srs2 in vivo. Here, we show that Srs2 indeed disrupts Rad51-containing complexes from chromosomes during meiosis. Overexpression of Srs2 during the meiotic prophase impairs meiotic recombination and removes Rad51 from meiotic chromosomes. This dismantling activity is specific for Rad51, as Srs2 Overexpression does not remove Dmc1 (a meiosis-specific Rad51 homolog), Rad52 (a Rad51 mediator), or replication protein A (RPA; a single-stranded DNA-binding protein). Rather, RPA replaces Rad51 under these conditions. A mutant Srs2 lacking helicase activity cannot remove Rad51 from meiotic chromosomes. Interestingly, the Rad51-binding domain of Srs2, which is critical for Rad51-dismantling activity in vitro, is not essential for this activity in vivo. Our results suggest that a precise level of Srs2, in the form of the Srs2 translocase, is required to appropriately regulate the Rad51 nucleoprotein filament dynamics during meiosis.     

Gene Network and Database for Genes of Wheat’s Resistance to Pathogenic Fungi

An overview describing a gene network that controls the formation of plant responses to diseases caused by pathogenic fungi (http://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet//viewer/Plant%20fungus%20pathogen.html) is presented. The gene network represents the coordinated interactions of genes, proteins, and regulatory molecules, including integrated defense mechanisms that prevent the development of infection, localize the lesion, and minimize damage. The gene network was reconstructed on the basis of literature data, and the elements of the gene network were associated with the records of the PGR database (Pathogenesis-Related Genes, http://srs6.bionet.nsc.ru/srs6bin/cgi-bin/wgetz?-page+top+-newId), where information on plant genes resistant to pathogenic fungi is accumulated. Reconstruction of the gene network allows us to formalize, visualize, and systematize possible mechanisms for the response of plant cells to fungal infection, which may be useful for the planning of experiments and interpretation of experimental data in this field of science.     

DNA Replication Checkpoint Signaling Depends on a Rad53–Dbf4 N-Terminal Interaction in Saccharomyces cerevisiae

Dbf4-dependent kinase (DDK) and cyclin-dependent kinase (CDK) are essential to initiate DNA replication at individual origins. During replication stress, the S-phase checkpoint inhibits the DDK- and CDK-dependent activation of late replication origins. Rad53 kinase is a central effector of the replication checkpoint and both binds to and phosphorylates Dbf4 to prevent late-origin firing. The molecular basis for the Rad53–Dbf4 physical interaction is not clear but occurs through the Dbf4 N terminus. Here we found that both Rad53 FHA1 and FHA2 domains, which specifically recognize phospho-threonine (pT), interacted with Dbf4 through an N-terminal sequence and an adjacent BRCT domain. Purified Rad53 FHA1 domain (but not FHA2) bound to a pT Dbf4 peptide in vitro, suggesting a possible phospho-threonine-dependent interaction between FHA1 and Dbf4. The Dbf4–Rad53 interaction is governed by multiple contacts that are separable from the Cdc5- and Msa1-binding sites in the Dbf4 N terminus. Importantly, abrogation of the Rad53–Dbf4 physical interaction blocked Dbf4 phosphorylation and allowed late-origin firing during replication checkpoint activation. This indicated that Rad53 must stably bind to Dbf4 to regulate its activity.     

Nucleoporin FG Domains Facilitate mRNP Remodeling at the Cytoplasmic Face of the Nuclear Pore Complex

Directional export of messenger RNA (mRNA) protein particles (mRNPs) through nuclear pore complexes (NPCs) requires multiple factors. In Saccharomyces cerevisiae, the NPC proteins Nup159 and Nup42 are asymmetrically localized to the cytoplasmic face and have distinct functional domains: a phenylalanine-glycine (FG) repeat domain that docks mRNP transport receptors and domains that bind the DEAD-box ATPase Dbp5 and its activating cofactor Gle1, respectively. We speculated that the Nup42 and Nup159 FG domains play a role in positioning mRNPs for the terminal mRNP-remodeling steps carried out by Dbp5. Here we find that deletion (Δ) of both the Nup42 and Nup159 FG domains results in a cold-sensitive poly(A)+ mRNA export defect. The nup42ΔFG nup159ΔFG mutant also has synthetic lethal genetic interactions with dbp5 and gle1 mutants. RNA cross-linking experiments further indicate that the nup42ΔFG nup159ΔFG mutant has a reduced capacity for mRNP remodeling during export. To further analyze the role of these FG domains, we replaced the Nup159 or Nup42 FG domains with FG domains from other Nups. These FG “swaps” demonstrate that only certain FG domains are functional at the NPC cytoplasmic face. Strikingly, fusing the Nup42 FG domain to the carboxy-terminus of Gle1 bypasses the need for the endogenous Nup42 FG domain, highlighting the importance of proximal positioning for these factors. We conclude that the Nup42 and Nup159 FG domains target the mRNP to Gle1 and Dbp5 for mRNP remodeling at the NPC. Moreover, these results provide key evidence that character and context play a direct role in FG domain function and mRNA export.     

The Principal Role of Ku in Telomere Length Maintenance Is Promotion of Est1 Association with Telomeres

Telomere length is tightly regulated in cells that express telomerase. The Saccharomyces cerevisiae Ku heterodimer, a DNA end-binding complex, positively regulates telomere length in a telomerase-dependent manner. Ku associates with the telomerase RNA subunit TLC1, and this association is required for TLC1 nuclear retention. Ku–TLC1 interaction also impacts the cell-cycle-regulated association of the telomerase catalytic subunit Est2 to telomeres. The promotion of TLC1 nuclear localization and Est2 recruitment have been proposed to be the principal role of Ku in telomere length maintenance, but neither model has been directly tested. Here we study the impact of forced recruitment of Est2 to telomeres on telomere length in the absence of Ku’s ability to bind TLC1 or DNA ends. We show that tethering Est2 to telomeres does not promote efficient telomere elongation in the absence of Ku–TLC1 interaction or DNA end binding. Moreover, restoration of TLC1 nuclear localization, even when combined with Est2 recruitment, does not bypass the role of Ku. In contrast, forced recruitment of Est1, which has roles in telomerase recruitment and activation, to telomeres promotes efficient and progressive telomere elongation in the absence of Ku–TLC1 interaction, Ku DNA end binding, or Ku altogether. Ku associates with Est1 and Est2 in a TLC1-dependent manner and enhances Est1 recruitment to telomeres independently of Est2. Together, our results unexpectedly demonstrate that the principal role of Ku in telomere length maintenance is to promote the association of Est1 with telomeres, which may in turn allow for efficient recruitment and activation of the telomerase holoenzyme.     

Identification of Citrus sinensis BAC clones containing genes relevant to fruit quality by two-dimensional overgo hybridization

As a complement to whole-genome sequencing efforts, we are comparing targeted genomic regions among sweet orange cultivars to identify coding and conserved noncoding regions, including regulatory elements, responsible for biological features unique to this species. Here, we report the identification of 1,018 bacterial artificial chromosome (BAC) clones containing genes relevant to fruit quality from a Citrus sinensis cv. “Vaniglia” 19.3X BAC library by two-dimensional 9?×?9 overgo hybridization. To design the overgo probes, we used the “C38” expressed sequence tag assembly (http://harvest.ucr.edu/) and OligoSpawn software (http://138.23.178.42). For BAC library screening, we selected 81 overgo probes associated with unigenes that putatively code for enzymes relevant to fruit quality (flavonol, anthocyanin, carotenoid, cellulose, starch, ascorbic acid, aromatic amino acid, and lignin biosynthesis; sucrose catabolism; glycolysis; oxidative/nonoxidative pentose phosphate pathway; fatty acid biosynthesis and oxidation; Krebs cycle). Hybridization probes were pooled and hybridized in groups of intersecting rows and columns to high-density BAC filters, followed by a deconvolution process that established BAC-probe addresses. BAC addresses were obtained for 75 of the 81 overgo probes initially selected, for a total of 1,018 BAC clones, a number consistent with the depth of coverage of the BAC library. BAC end sequencing was carried out, and end-sequence pairs were mapped to their best location in the Citrus clementina genome sequence assembly using the comparative genomic database Phytozome (http://www.phytozome.net/). The BAC clones corresponding to each probe were mapped within the same scaffold as the target gene, demonstrating that the approach we used was successful in isolating the targeted genomic regions.     

Bioinformatics Approach to Evaluate Differential Gene Expression of M1/M2 Macrophage Phenotypes and Antioxidant Genes in Atherosclerosis

Atherosclerosis is a pro-inflammatory process intrinsically related to systemic redox impairments. Macrophages play a major role on disease development. The specific involvement of classically activated, M1 (pro-inflammatory), or the alternatively activated, M2 (anti-inflammatory), on plaque formation and disease progression are still not established. Thus, based on meta-data analysis of public micro-array datasets, we compared differential gene expression levels of the human antioxidant genes (HAG) and M1/M2 genes between early and advanced human atherosclerotic plaques, and among peripheric macrophages (with or without foam cells induction by oxidized low density lipoprotein, oxLDL) from healthy and atherosclerotic subjects. Two independent datasets, GSE28829 and GSE9874, were selected from gene expression omnibus (http://www.ncbi.nlm.nih.gov/geo/) repository. Functional interactions were obtained with STRING (http://string-db.org/) and Medusa (http://coot.embl.de/medusa/). Statistical analysis was performed with ViaComplex^® (http://lief.if.ufrgs.br/pub/biosoftwares/viacomplex/) and gene score enrichment analysis (http://www.broadinstitute.org/gsea/index.jsp). Bootstrap analysis demonstrated that the activity (expression) of HAG and M1 gene sets were significantly increased in advance compared to early atherosclerotic plaque. Increased expressions of HAG, M1, and M2 gene sets were found in peripheric macrophages from atherosclerotic subjects compared to peripheric macrophages from healthy subjects, while only M1 gene set was increased in foam cells from atherosclerotic subjects compared to foam cells from healthy subjects. However, M1 gene set was decreased in foam cells from healthy subjects compared to peripheric macrophages from healthy subjects, while no differences were found in foam cells from atherosclerotic subjects compared to peripheric macrophages from atherosclerotic subjects. Our data suggest that, different to cancer, in atherosclerosis there is no M1 or M2 polarization of macrophages. Actually, M1 and M2 phenotype are equally induced, what is an important aspect to better understand the disease progression, and can help to develop new therapeutic approaches.