Lipid rafts as platforms for sphingosine 1-phosphate metabolism and signalling

Spontaneous segregation of cholesterol and sphingolipids as a liquid-ordered phase leads to their clustering in selected membrane areas, the lipid rafts. These specialized membrane domains enriched in gangliosides, sphingomyelin, cholesterol and selected proteins involved in signal transduction, organize and determine the function of multiprotein complexes involved in several aspects of signal transduction, thus regulating cell homeostasis. Sphingosine 1-phosphate, an important biologically active mediator, is involved in several signal transduction processes regulating a plethora of cell functions and, not only several of its downstream effectors tend to localize in lipid rafts, some of the enzymes involved in its pathway, of receptors involved in its signalling and its transporters have been often found in these membrane microdomains. Considering this, in this review we address what is currently known regarding the relationship between sphingosine 1-phosphate metabolism and signalling and plasma membrane lipid rafts.     

Biosynthesis of pectin

Pectin consists of a group of acidic polysaccharides that constitute a large part of the cell wall of plants. The pectic polysaccharides have a complex structure but can generally be divided into homogalacturonan, rhamnogalacturonan I, rhamnogalacturonan II (RGII) and xylogalacturonan (XGA). These polysaccharides appear to be present in all cells but their relative abundance and structural details differ between cell types and species. Pectin is synthesized in the Golgi vesicles and its complexity dictates that a large number of enzymes must be involved in the process. The biosynthetic enzymes required are glycosyltransferases and decorating enzymes including methyltransferases, acetyltransferases and feruloyltransferases. Biochemical methods successfully led to the recent identification of a pectin biosynthetic galacturonosyltransferase (GAUT1), and recent functional genomics and mutant studies have allowed the identification of several biosynthetic enzymes involved in making different parts of pectin. Strong evidence has been obtained for two xylosyltransferases (RGXT1 and RGXT2) with documented in vitro activity and apparently involved in making a side chain of RGII. Strong circumstantial evidence has been obtained for a putative glucuronosyltransferase (GUT1) involved in making RGII, a putative arabinosyltransferase (ARAD1) involved in making arabinan, and a putative xylosyltransferase (XGD1) involved in making XGA. In several other cases, enzymes have been identified as involved in making pectin but because of ambiguity in the cell wall compositions of mutants and lack of direct biochemical evidence their specific activities are more uncertain.     

Developmental constraint on gene duplicability in fruit flies and nematodes

A previous study in nematodes suggested that developmental constraint reduces the duplicability of genes involved in early development. Recent large-scale gene expression studies of fly development enabled us to conduct a more detailed study of this issue. We found that the average duplicability of genes involved in embryonic development is indeed lower than that of genes involved in larval development but not significantly lower than that of genes involved in later stages of development. Moreover, in both flies and nematodes genes with multiple expression peaks do not seem to have a lower duplicability than do genes with a single expression peak. Thus, although developmental constraint does appear to reduce gene duplicability, the effect seems weak or at best moderate.     

Sperm membrane physiology and relevance for fertilization

This paper aims to overview recent insights in sperm surface remodelling pertinent to fertilization. A basic understanding of this remodelling is required to interpret the high amount of data appearing from high-throughput identification techniques for proteins presently applied in reproductive biology. From the extensive lists of protein candidates identified by proteomics, only a few are recognized to be directly involved in fertilization. Others are indirectly involved, but many are not yet considered to be involved in fertilization. Some of these newly identified and unexpected proteins may shed new light in the current molecular models for fertilization. However, the gathered lists of sperm proteins possibly involved in fertilization do only tell a part of the story regarding how fertilization is accomplished. When considering the identification of proteins involved in fertilization, one also needs to take into account the fundamental mechanisms involved in the redistribution of sperm surface proteins in membrane protein complexes and the involvement of cell signalling events that regulate their post-translational modification status. Both processes are likely requisite for protein configuration and grouping into functional membrane protein complexes necessary to elicit their delicate roles in fertilization. This paper emphasizes biochemical models for membrane surface modelling and their potential involvement for remodelling the sperm surface in the above described processes.     

The identification of genes involved in the stomatal response to reduced atmospheric relative humidity

Stomatal pores of higher plants close in response to decreases in atmospheric relative humidity (RH). This is believed to be a mechanism that prevents the plant from losing excess water when exposed to a dry atmosphere and as such is likely to have been of evolutionary significance during the colonization of terrestrial environments by the embryophytes. We have conducted a genetic screen, based on infrared thermal imaging, to identify Arabidopsis genes involved in the stomatal response to reduced RH. Here we report the characterization of two genes, identified during this screen, which are involved in the guard cell reduced RH signaling pathway. Both genes encode proteins known to be involved in guard cell ABA signaling. OST1 encodes a protein kinase involved in ABA-mediated stomatal closure while ABA2 encodes an enzyme involved in ABA biosynthesis. These results suggest, in contrast to previously published work, that ABA plays a role in the signal transduction pathway connecting decreases in RH to reductions in stomatal aperture. The identification of OST1 as a component required in stomatal RH and ABA signal transduction supports the proposition that guard cell signaling is organized as a network in which some intracellular signaling proteins are shared among different stimuli.     

鉴别杰多霉素生物合成后修饰氧化酶JadH中参与底物结合或催化的关键残基

JadH是羟化脱水双功能酶,参与杰多霉素生物合成中的聚酮后修饰反应,将2,3-dehydro-UWM6催化为dehydrorabelomycin。为了分析杰多霉素生物合成途径中后修饰氧化酶JadH结合、催化底物的关键氨基酸,构建了JadH与底物复合物的三维结构模型。利用该模型并结合JadH同源蛋白氨基酸序列比对分析,推测出JadH活性中心中可能参与底物结合或催化的关键氨基酸(R50、G51、L52、G53、F100、R221、I223、P295和G298)。通过定点突变及体外酶学实验对这些位点的突变体的催化活性进行评价,结果显示这些突变株活性均显著低于野生型,表明这9个氨基酸是JadH参与底物结合或催化的关键氨基酸。     

Flexibility in photosynthetic electron transport: a newly identified chloroplast oxidase involved in chlororespiration

Besides electron transfer reactions involved in the 'Z' scheme of photosynthesis, alternative electron transfer pathways have been characterized in chloroplasts. These include cyclic electron flow around photosystem I (PS I) or a respiratory chain called chlororespiration. Recent work has supplied new information concerning the molecular nature of the electron carriers involved in the non-photochemical reduction of the plastoquinone (PQ) pool. However, until now little is known concerning the nature of the electron carriers involved in PQ oxidation. By using mass spectrometric measurement of oxygen exchange performed in the presence of 18O-enriched O2 and Chlamydomonas mutants deficient in PS I, we show that electrons can be directed to a quinol oxidase sensitive to propyl gallate but insensitive to salicyl hydroxamic acid. This oxidase has immunological and pharmacological similarities with a plastid protein involved in carotenoid biosynthesis.     

Identification of novel genes associated with conidiation in Beauveria bassiana with suppression subtractive hybridization

The conidiation of the entomopathogenic fungus Beauveria bassiana (Hyphomycete) is a complex process that involves the stage- and cell-type-specific expression of hundreds of genes. The suppression subtractive hybridization method was used to target genes involved in conidiation. Seventeen genes were cloned that potentially were involved in conidia formation. Six of them demonstrated differential expression between conidial and vegetative cultures. Sequence analysis showed three cDNA fragments had similarity to known genes involved in either cellular metabolism or cell regulatory processes. The other cDNA fragments showed low or no similarity to any genes previously described. The full-length cDNA and genomic sequence of a gene designated A43 was isolated. The A43 protein is composed of 180 amino acids and has 34% identity to a RNA-binding region-containing protein. The temporal expression pattern was consistent with the gene being involved in conidiation. The colony morphology of the A43 knock-out mutant had more floccus mycelium than the wild-type and also produced fewer conidia, indicating the A43 gene is involved in B. bassiana conidiation.     

CONSUMER INVOLVEMENT AND EVALUATION OF GREEN PEAS1

This paper reports the effect of consumer involvement on overall acceptance of frozen peas used in green salad and the effect of consumer involvement on the consumer's ability to perceive variations in a set of physical/chemical characteristics such as AIS (Alcohol Insoluble Solids) and color. The results reveal that consumers with high involvement evaluate 16 experimentally varied pea samples more in accordance with quality indicators used in the industry than consumers with low involvement. In our study 61% of the consumers were highly involved. For low involved consumers there was no relation between average acceptance and the quality indicators used by producer/retailer and retailer/consumer. High involved consumers could identify more of the physical/chemical variation in the pea samples than the low involved consumers. The results stress the importance of a preliminary segmentation of consumers. The low involved consumers do not seem to have any specific preferences for any of the samples included in the study although samples are varied considerably with respect to size, color and amount of sucrose. It may be considered as indifference. An obvious conclusion to draw from the results of this study is to concentrate on the highly involved consumers in further product development.     

Keratinocyte cultures from involved skin in vitiligo patients show an impaired in vitro behaviour

Vitiligo depigmentation is considered a consequence of either melanocyte disappearance or loss of functioning melanocytes in the involved areas. However, it has been reported that keratinocytes in involved vitiligo skin are damaged too. Based on this evidence, we evaluated the in vitro behaviour, in life span cultures, of involved and uninvolved vitiligo keratinocytes and their expression of proliferation, differentiation and senescence markers. An additional purpose was to investigate whether vitiligo keratinocytes from depigmented skin are able to sustain survival and growth of normal melanocytes (when added in co-culture experiments), as normal human keratinocytes manage to do. Our results demonstrate that almost all involved vitiligo keratinocytes have a shorter life span in vitro than the uninvolved cells and all of them do not maintain melanocytes in culture in a physiological ratio. Modification of proliferation and senescence marker expression also occurs. Indeed, we detected low initial expression levels of the senescence marker p16 in involved vitiligo keratinocytes, despite their shorter in vitro life span, and increased expression of proliferating cell nuclear antigen and p53. This preliminary analysis of a small number of in vitro cultured vitiligo keratinocytes suggests an impaired senescence process in lesional vitiligo keratinocytes and attempts to regulate it.     

Processing of heme and heme-containing proteins by bacteria

An extensive amount of new knowledge on bacterial systems involved in heme processing has been accumulated in the last 10 years. We discuss common themes in heme transport across bacterial outer and inner membranes, emphasizing proteins and mechanisms involved. The processing of heme in the bacterial cytoplasm is extensively covered, and a new hypothesis about the fate of heme in the bacterial cell is presented. Auxiliary genes involved in heme utilization, i.e., TonB, proteases, proteins involved in heme storage and pigmentation, as well as genes involved in regulation of heme assimilation are reviewed.     

Comparative genomics of hemiascomycete yeasts: genes involved in DNA replication, repair, and recombination

Among genes conserved from bacteria to mammals are those involved in replicating and repairing DNA. Following the complete sequencing of four hemiascomycetous yeast species during the course of the Genolevures 2 project, we have studied the conservation of 106 genes involved in replication, repair, and recombination in Candida glabrata, Kluyveromyces lactis, Debaryomyces hansenii, and Yarrowia lipolytica and compared them with their Saccharomyces cerevisiae orthologues. We found that proteins belonging to the replication fork and to the nucleotide excision repair pathway were-on the average-more conserved than proteins involved in the checkpoint response to DNA damage or in meiotic recombination. The meiotic recombination proteins Spo11p and Mre11p-Rad50p, involved in making meiotic double-strand breaks (DSBs), are conserved as is Mus81p, involved in resolving meiotic recombination intermediates. Interestingly, genes found in organisms in which DSB-repair is required for proper synapsis during meiosis are also found in C. glabrata, K. lactis, and D. hansenii but not in Y. lipolytica, suggesting that two modes of meiotic recombination have been selected during evolution of the hemiascomycetous yeasts. In addition, we found that SGS1 and TOP1, respectively, a DEAD/DEAH helicase and a type I topoisomerase, are duplicated in C. glabrata and that SRS2, a helicase involved in homologous recombination, is tandemly duplicated in K. lactis. Phylogenetic analyses show that the duplicated SGS1 gene evolved faster than the original gene, probably leading to a specialization of function of the duplicated copy.     

Evolution and diversity of the 2–oxoglutarate‐dependent dioxygenase superfamily in plants

The 2–oxoglutarate‐dependent dioxygenase (2OGD) superfamily is the second largest enzyme family in the plant genome, and its members are involved in various oxygenation/hydroxylation reactions. Despite their biochemical significance in metabolism, a systematic analysis of plant 2OGDs remains to be accomplished. We present a phylogenetic classification of 479 2OGDs in six plant models, ranging from green algae to angiosperms. These were classified into three classes – DOXA, DOXB and DOXC – based on amino acid sequence similarity. The DOXA class includes plant homologs of Escherichia coli AlkB, which is a prototype of 2OGD involved in the oxidative demethylation of alkylated nucleic acids and histones. The DOXB class is conserved across all plant taxa and is involved in proline 4–hydroxylation in cell wall protein synthesis. The DOXC class is involved in specialized metabolism of various phytochemicals, including phytohormones and flavonoids. The vast majority of 2OGDs from land plants were classified into the DOXC class, but only seven from Chlamydomonas, suggesting that this class has diversified during land plant evolution. Phylogenetic analysis assigned DOXC‐class 2OGDs to 57 phylogenetic clades. 2OGD genes involved in gibberellin biosynthesis were conserved among vascular plants, and those involved in flavonoid and ethylene biosynthesis were shared among seed plants. Several angiosperm‐specific clades were found to be involved in various lineage‐specific specialized metabolisms, but 31 of the 57 DOXC‐class clades were only found in a single species. Therefore, the evolution and diversification of DOXC‐class 2OGDs is partly responsible for the diversity and complexity of specialized metabolites in land plants.     

CD133 protein N-glycosylation processing contributes to cell surface recognition of the primitive cell marker AC133 epitope

The AC133 epitope expressed on the CD133 glycoprotein has been widely used as a cell surface marker of numerous stem cell and cancer stem cell types. It has been recently proposed that posttranslational modification and regulation of CD133 may govern cell surface AC133 recognition. Therefore, we performed a large scale pooled RNA interference (RNAi) screen to identify genes involved in cell surface AC133 expression. Gene hits could be validated at a rate of 70.5% in a secondary assay using an orthogonal RNAi system, demonstrating that our primary RNAi screen served as a powerful genetic screening approach. Within the list of hits from the primary screen, genes involved in N-glycan biosynthesis were significantly enriched as determined by Ingenuity Canonical Pathway analyses. Indeed, inhibiting biosynthesis of the N-glycan precursor using the small molecule tunicamycin or inhibiting its transfer to CD133 by generating N-glycan-deficient CD133 mutants resulted in undetectable cell surface AC133. Among the screen hits involved in N-glycosylation were genes involved in complex N-glycan processing, including the poorly characterized MGAT4C, which we demonstrate to be a positive regulator of cell surface AC133 expression. Our study identifies a set of genes involved in CD133 N-glycosylation as a direct contributing factor to cell surface AC133 recognition and provides biochemical evidence for the function and structure of CD133 N-glycans.     

Key genes and functional coexpression modules involved in the pathogenesis of systemic lupus erythematosus

We performed a systematic review of genome‐wide gene expression datasets to identify key genes and functional modules involved in the pathogenesis of systemic lupus erythematosus (SLE) at a systems level. Genome‐wide gene expression datasets involving SLE patients were searched in Gene Expression Omnibus and ArrayExpress databases. Robust rank aggregation (RRA) analysis was used to integrate those public datasets and identify key genes associated with SLE. The weighted gene coexpression network analysis (WGCNA) was adapted to identify functional modules involved in SLE pathogenesis, and the gene ontology enrichment analysis was utilized to explore their functions. The aberrant expressions of several randomly selected key genes were further validated in SLE patients through quantitative real‐time polymerase chain reaction. Fifteen genome‐wide gene expression datasets were finally included, which involved a total of 1,778 SLE patients and 408 healthy controls. A large number of significantly upregulated or downregulated genes were identified through RRA analysis, and some of those genes were novel SLE gene signatures and their molecular roles in etiology of SLE remained vague. WGCNA further successfully identified six main functional modules involved in the pathogenesis of SLE. The most important functional module involved in SLE included 182 genes and mainly enriched in biological processes, including defense response to virus, interferon signaling pathway, and cytokine‐mediated signaling pathway. This study identifies a number of key genes and functional coexpression modules involved in SLE, which provides deepening insights into the molecular mechanism of SLE at a systems level and also provides some promising therapeutic targets.     

Identification and functions of amino acid residues in PotB and PotC involved in spermidine uptake activity

Amino acid residues on PotB and PotC involved in spermidine uptake were identified by random and site-directed mutagenesis. It was found that Trp(8), Tyr(43), Trp(100), Leu(110), and Tyr(261) in PotB and Trp(46), Asp(108), Glu(169), Ser(196), Asp(198), and Asp(199) in PotC were strongly involved in spermidine uptake and that Tyr(160), Glu(172), and Leu(274) in PotB and Tyr(19), Tyr(88), Tyr(148), Glu(160), Leu(195), and Tyr(211) in PotC were moderately involved in spermidine uptake. Among 11 amino acid residues that were strongly involved in spermidine uptake, Trp(8) in PotB was important for insertion of PotB and PotC into membranes. Tyr(43), Trp(100), and Leu(110) in PotB and Trp(46), Asp(108), Ser(196), and Asp(198) in PotC were found to be involved in the interaction with PotD. Leu(110) and Tyr(261) in PotB and Asp(108), Asp(198), and Asp(199) in PotC were involved in the recognition of spermidine, and Trp(100) and Tyr(261) in PotB and Asp(108), Glu(169), and Asp(198) in PotC were involved in ATPase activity of PotA. Accordingly, Trp(100) in PotB was involved in both PotD recognition and ATPase activity, Leu(110) in PotB was involved in both PotD and spermidine recognition, and Tyr(261) in PotB was involved in both spermidine recognition and ATPase activity. Asp(108) and Asp(198) in PotC were involved in PotD and spermidine recognition as well as ATPase activity. These results suggest that spermidine passage from PotD to the cytoplasm is coupled to the ATPase activity of PotA through a structural change of PotA by its ATPase activity.     

Characterization of the interaction between beta 2-glycoprotein I and mitochondria, platelets, liposomes and bile acids

Several different binding mechanisms appear to be involved in the binding of beta 2-glycoprotein I to biological membranes. One of these mechanisms is a hydrophilic interaction between negatively-charged phospholipids in the membrane and histidine residues in beta 2-glycoprotein I. This mechanism seems to be involved in binding of the protein to mitochondria but not to platelets. Another mechanism may involve a site on beta 2-glycoprotein I, which binds to the steroid ring system particularly to such steroids not having a 7-hydroxy group. This type of binding may be involved in the interaction between beta 2-glycoprotein I and platelets as well as mitochondria.