Genome Analysis of Pseudomonas fluorescens PCL1751: A Rhizobacterium that Controls Root Diseases and Alleviates Salt Stress for Its Plant Host

Pseudomonas fluorescens PCL1751 is a rod-shaped Gram-negative bacterium isolated from the rhizosphere of a greenhouse-grown tomato plant in Uzbekistan. It controls several plant root diseases caused by Fusarium fungi through the mechanism of competition for nutrients and niches (CNN). This mechanism does not rely on the production of antibiotics, so it avoids the concerns of resistance development and is environmentally safe. Additionally, this bacterium promotes plant growth by alleviating salt stress for its plant host. To investigate the genetic mechanisms that may explain these observations, we determined the complete genome sequence of this bacterium, examined its gene content, and performed comparative genomics analysis with other Pseudomonas strains. The genome of P. fluorescens PCL1751 consisted of one circular chromosome that is 6,143,950 base-pairs (bp) in size; no plasmid was found. The annotation included 19 rRNA, 70 tRNA, and 5,534 protein-coding genes. The gene content analysis identified a large number of genes involved in chemotaxis and motility, colonization of the rhizosphere, siderophore biosynthesis, and osmoprotectant production. In contrast, the pathways involved in the biosynthesis of phytohormones or antibiotics were not found. Comparison with other Pseudomonas genomes revealed extensive variations in their genome size and gene content. The presence and absence of secretion system genes were highly variable. As expected, the synteny conservation among strains decreased as a function of phylogenetic divergence. The integration of prophages appeared to be an important driver for genome rearrangements. The whole-genome gene content analysis of this plant growth-promoting rhizobacterium (PGPR) provided some genetic explanations to its phenotypic characteristics. The extensive and versatile substrate utilization pathways, together with the presence of many genes involved in competitive root colonization, provided further support for the finding that this strain achieves biological control of pathogens through effective competition for nutrients and niches.     

Mutations in the EPHA2 Gene Are a Major Contributor to Inherited Cataracts in South-Eastern Australia

Congenital cataract is the most common cause of treatable visual impairment in children worldwide. Mutations in many different genes lead to congenital cataract. Recently, mutations in the receptor tyrosine kinase gene, EPHA2, have been found to cause congenital cataract in six different families. Although these findings have established EPHA2 as a causative gene, the total contribution of mutations in this gene to congenital cataract is unknown. In this study, for the first time, a population-based approach was used to investigate the frequency of disease causing mutations in the EPHA2 gene in inherited cataract cases in South-Eastern Australia. A cohort of 84 familial congenital or juvenile cataract index cases was screened for mutations in the EPHA2 gene by direct sequencing. Novel changes were assessed for segregation with the disease within the family and in unrelated controls. Microsatellite marker analysis was performed to establish any relationship between families carrying the same mutation. We report a novel congenital cataract causing mutation c.1751C>T in the EPHA2 gene and the previously reported splice mutation c.2826-9G>A in two new families. Additionally, we report a rare variant rs139787163 potentially associated with increased susceptibility to cataract. Thus mutations in EPHA2 account for 4.7% of inherited cataract cases in South-Eastern Australia. Interestingly, the identified rare variant provides a link between congenital and age-related cataract.     

AglC and AglK are involved in biosynthesis and attachment of diacetylated glucuronic acid to the N-glycan in Methanococcus voltae

Recent advances in the field of prokaryotic N-glycosylation have established a foundation for the pathways and proteins involved in this important posttranslational protein modification process. To continue the study of the Methanococcus voltae N-glycosylation pathway, characteristics of known eukaryotic, bacterial, and archaeal proteins involved in the N-glycosylation process were examined and used to select candidate M. voltae genes for investigation as potential glycosyl transferase and flippase components. The targeted genes were knocked out via linear gene replacement, and the resulting effects on N-glycan assembly were identified through flagellin and surface (S) layer protein glycosylation defects. This study reports the finding that deletion of two putative M. voltae glycosyl transferase genes, designated aglC (for archaeal glycosylation) and aglK, interfered with proper N-glycosylation. This resulted in flagellin and S-layer proteins with significantly reduced apparent molecular masses, loss of flagellar assembly, and absence of glycan attachment. Given previous knowledge of both the N-glycosylation pathway in M. voltae and the general characteristics of N-glycosylation components, it appears that AglC and AglK are involved in the biosynthesis or transfer of diacetylated glucuronic acid within the glycan structure. In addition, a knockout of the putative flippase candidate gene (Mv891) had no effect on N-glycosylation but did result in the production of giant cells with diameters three to four times that of wild-type cells.     

Diseases of maize in the wet lowland tropics and the collapse of the Classic Maya civilization

The Classic Maya civilization was centered in lowlands of the Petén in northern Guatemala, and collapsed mysteriously in the ninth century AD. Abandoned were rich agricultural lands carved without metal tools out of a tropical rain forest, lands that had been farmed with increasing intensity for six to sixteen centuries. The Maya evidently resettled in highlands to the south or in less productive dry lowlands to the north. No reoccupation occurred of the Petén farms, homes or ceremonial centers until their discovery in the past two centuries. Sustained crop failure of maize (Zen mavs L.) due to an epidemic of the planthopper-borne virus, maize mosaic virus (MMV), is proposed as a primary contributing cause of the collapse. Major diseases and pests of maize in the tropics are assessed for their relative significance in and near the Petén vs. the highlands, and the viruses are highlighted. Maize mosaic virus is a devastating virus disease transmitted by the corn planthopper,Peregrinus maidis, an insect restricted to tropic lowlands. Maize and teosinte are its only definitively known hosts. Thus the disease has been serious only where maize is grown more-or-less continuously through the year in wet or irrigated tropics (e.g., Caribbean Islands, Venezuela, Hawaii, Tanzania, Australia). It is reported here for southern Mexico and the Petén of Guatemala. Resistance in maize occurs only in one known form, the gene Mv. that confers a high level resistance but not immunity. Resistance data are presented for 63 of the 67 races of maize thought to have evolved in the Northern Hemisphere. The Mv gene is shown to occur in all seven of the races of maize evolved in the Caribbean, but in none of the primitive Mexican or Central American races. It is proposed that maize mosaic virus originated in northern South America at or about the time maize was brought into the Caribbean by the Arawak around the time of Christ. The sympatric origin or selection in maize of the Mv resistance mutant in this region is assumed to have led to its incorporation in all seven Caribbean maize races. It is conjectured that viruliferous leafhoppers were blown from the Caribbean into the Petén around the eighth century allowing the disease to become epidemic in susceptible maize races such as Nal-Tel and Tepecintle, grown by the Petén Maya. Sustained failure of maize production due to MMV would have characterized areas of intensive maize cultivation, particularly where it was year-round. The disease would have been less severe in areas with a long dry season, as to the north of Yucatán and it would not have occurred in the highland areas to the south and west, areas to which surviving Maya presumably migrated.     

Root and leaf traits, water use and drought tolerance of maize genotypes

The main components of drought tolerance of six maize genotypes were studied to evaluate crop performance in water limiting environments: (1) the postponement of dehydration by reduced transpiration rate (TR) and an increased efficiency of water acquisition from soil; (2) the tolerance of dehydration by effective physiological water use. The aim was to describe the genotype dependent response to drought in leaf and root traits and water relations using data from controlled environment and field experiments, and using dynamic simulation by the Swedish Coup model. High genetic variation was detected in the root density, acquisition efficiency and water use among the genotypes. The female parent lines had the greatest TR with the smallest dry matter accumulation in water deficiency, whereas hybrids could acquire more water from dryer soil while maintaining a lower TR. Hybrid Mv 444 increased water potential more strongly in leaves than hybrid Norma. The postponement of dehydration was observed for Norma, while more tolerance to dehydration characterized Mv 444. Simulation was an effective tool for testing hypotheses considering water acquisition efficiency and for summarizing the results of the measurements in a formalized structure; it helped to quantify the dynamics of water availability and the impact of drought on the growth of the maize genotypes.     

Identification of Two Novel Mutations in the PHEX Gene in Chinese Patients with Hypophosphatemic Rickets/Osteomalacia

Objective

X-linked dominant hypophosphatemia (XLH) is the most prevalent form of inherited rickets/osteomalacia in humans. The aim of this study was to identify PHEX gene mutations and describe the clinical features observed in 6 unrelated Chinese families and 3 sporadic patients with hypophosphatemic rickets/osteomalacia.

Methods

For this study, 45 individuals from 9 unrelated families of Chinese Han ethnicity (including 16 patients and 29 normal phenotype subjects), and 250 healthy donors were recruited. All 22 exons and exon-intron boundaries of the PHEX gene were amplified by polymerase chain reaction (PCR) and directly sequenced.

Results

The PHEX mutations were detected in 6 familial and 3 sporadic hypophosphatemic rickets/osteomalacia. Altogether, 2 novel mutations were detected: 1 missense mutation c.1183G>C in exon 11, resulting in p.Gly395Arg and 1 missense mutation c.1751A>C in exon 17, resulting in p.His584Pro. No mutations were found in the 250 healthy controls.

Conclusions

Our study increases knowledge of the PHEX gene mutation types and clinical phenotypes found in Chinese patients with XLH, which is important for understanding the genetic basis of XLH. The molecular diagnosis of a PHEX genetic mutation is of great importance for confirming the clinical diagnosis of XLH, conducting genetic counseling, and facilitating prenatal intervention, especially in the case of sporadic patients.     

Comparison of Different Cell Substrates on the Measurement of Human Influenza Virus Neutralizing Antibodies

Eight cell lines were systematically compared for their permissivity to primary infection, replication, and spread of seven human influenza viruses. Cell lines were of human origin (Caco-2, A549, HEp-2, and NCI-H292), monkey (Vero, LLC-MK2), mink (Mv1 Lu), and canine (MDCK). The influenza viruses included seasonal types and subtypes and a pandemic virus. The MDCK, Caco-2, and Mv1 Lu cells were subsequently compared for their capacity to report neutralization titers at day one, three and six post-infection. A gradient of sensitivity to primary infection across the eight cell lines was observed. Relative to MDCK cells, Mv1 Lu reported higher titers and the remaining six cell lines reported lower titers. The replication and spread of the seven influenza viruses in the eight cell substrates was determined using hemagglutinin expression, cytopathic effect, and neuraminidase activity. Virus growth was generally concordant with primary infection, with a gradient in virus replication and spread. However, Mv1 Lu cells poorly supported virus growth, despite a higher sensitivity to primary infection. Comparison of MDCK, Caco-2, and Mv1 Lu in neutralization assays using defined animal antiserum confirmed MDCK cells as the preferred cell substrate for influenza virus testing. The results observed for neutralization at one day post-infection showed MDCK cells were similar (<1 log₂ lower) or superior (>1 log₂ higher) for all seven viruses. Relative to Caco-2 and Mv1 Lu cells, MDCK generally reported the highest titers at three and six days post-infection for the type A viruses and lower titers for the type B viruses and the pandemic H9N2 virus. The reduction in B virus titer was attributed to the complete growth of type B viruses in MDCK cells before day three post-infection, resulting in the systematic underestimation of neutralization titers. This phenomenon was also observed with Caco-2 cells.     

Physiological response of wheat varieties to elevated atmospheric CO2 and low water supply levels

In the phytotron experiment, the effect of elevated atmospheric CO₂ (EC, 750 μmol mol^?1) on the drought tolerance was studied in two winter varieties (Mv Mambo, tolerant; Mv Regiment, moderately tolerant) and in one spring variety of wheat (Lona, sensitive to drought). Changes in net photosynthetic rate (P _N), stomatal conductance, transpiration, wateruse efficiency, effective quantum yield of photosystem II, and activities of glutathione reductase (GR), glutathione-Stransferase (GST), guaiacol peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) were monitored during water withdrawal. Drought caused a faster decline of P _N at EC, leading to the lower assimilation rates under severe drought compared with ambient CO₂ (NC). In the sensitive variety, P _N remained high for a longer period at EC. The growth at EC resulted in a more relaxed activation level of the antioxidant enzyme system in all three varieties, with very low activities of GR, GST, APX, and POD. The similar, low values were due to decreases in the varieties which had higher ambient values. A parallel increase of CAT was, however, recorded in two varieties. As the decline in P _N was faster at EC under drought but there was no change in the rate of electron transport compared to NC values, a higher level of oxidative stress was induced. This triggered a more pronounced, general response in the antioxidant enzyme system at EC, leading to very high activities of APX, CAT, and GST in all three varieties. The results indicated that EC had generally favourable effects on the development and stress tolerance of plants, although bigger foliage made the plants more prone to the water loss. The relaxation of the defence mechanisms increased potentially the risk of damage due to the higher level of oxidative stress at EC under severe drought compared with NC.     

SPARC inhibits epithelial cell proliferation in part through stimulation of the transforming growth factor-beta-signaling system

Secreted protein, acidic and rich in cysteine (SPARC) is a multifunctional secreted protein that regulates cell-cell and cell-matrix interactions, leading to alterations in cell adhesion, motility, and proliferation. Although SPARC is expressed in epithelial cells, its ability to regulate epithelial cell growth remains largely unknown. We show herein that SPARC strongly inhibited DNA synthesis in transforming growth factor (TGF)-beta-sensitive Mv1Lu cells, whereas moderately inhibiting that in TGF-beta-insensitive Mv1Lu cells (i.e., R1B cells). Overexpression of dominant-negative Smad3 in Mv1Lu cells, which abrogated growth arrest by TGF-beta, also attenuated growth arrest stimulated by SPARC. Moreover, the extracellular calcium-binding domain of SPARC (i.e., SPARC-EC) was sufficient to inhibit Mv1Lu cell proliferation but not that of R1B cells. Similar to TGF-beta and thrombospondin-1, treatment of Mv1Lu cells with SPARC or SPARC-EC stimulated Smad2 phosphorylation and Smad2/3 nuclear translocation: the latter response to all agonists was abrogated in R1B cells or by pretreatment of Mv1Lu cells with neutralizing TGF-beta antibodies. SPARC also stimulated Smad2 phosphorylation in MB114 endothelial cells but had no effect on bone morphogenetic protein-regulated Smad1 phosphorylation in either Mv1Lu or MB114 cells. Finally, SPARC and SPARC-EC stimulated TGF-beta-responsive reporter gene expression through a TGF-beta receptor- and Smad2/3-dependent pathway in Mv1Lu cells. Collectively, our findings identify a novel mechanism whereby SPARC inhibits epithelial cell proliferation by selectively commandeering the TGF-beta signaling system, doing so through coupling of SPARC-EC to a TGF-beta receptor- and Smad2/3-dependent pathway.     

A study of the strength and stability of gas vesicles isolated from a blue-green alga

Summary Acid phosphatase was studied by means of electron microscope cytochemistry in glutaraldehyde-fixed myxamoebae of Dictyostelium discoideum grown on dead bacteria. The enzyme activity was localized to the digestive vacuoles in vegetative as well as in aggregating cells. Biochemical experiments showed that the enzyme was not inactivated by fixation in 2% purified glutaraldehyde.Abbreviations used NPP p-nitrophenyl phosphate - NP p-nitrophenol - GP -glycerophosphate - glc-6-P glucose-6-phosphate - Pi orthophosphate     

基于相邻木排列关系的混交度研究

混交度是反映森林群落中树种相互隔离状况的一个重要指标,目前已提出多种混交度指数.Mg考虑了对象木与最近相邻木的树种异同,Mv和Ms进一步考虑了最近相邻木(空间结构单元)树种数,但仍不能准确描述树种隔离程度.基于相邻木排列关系的混交度Mp,利用“1+4”结构的17个不同空间结构单元和天目山常绿阔叶林数据对Mg、Mv、Ms和Mp4个混交度进行了比较分析.结果表明:Mp的区分能力最强,Mv和Ms次之,Mg最差.Mp最适用于分析混交结构复杂的林分.在天目山常绿阔叶林分析中,混交度水平为中度,4个最近邻体中有2个相同种顺序排列的空间结构单元个数明显多于交错排列的个数.基于相邻木排列关系的混交度Mp能准确区分树种隔离程度,提高了混交度的区分度,可反映森林实际混交状况.     

Regulation of Endo-Acting Glycosyl Hydrolases in the Hyperthermophilic Bacterium Thermotoga maritima Grown on Glucan- and Mannan-Based Polysaccharides

The genome sequence of the hyperthermophilic bacterium Thermotoga maritima encodes a number of glycosyl hydrolases. Many of these enzymes have been shown in vitro to degrade specific glycosides that presumably serve as carbon and energy sources for the organism. However, because of the broad substrate specificity of many glycosyl hydrolases, it is difficult to determine the physiological substrate preferences for specific enzymes from biochemical information. In this study, T. maritima was grown on a range of polysaccharides, including barley β-glucan, carboxymethyl cellulose, carob galactomannan, konjac glucomannan, and potato starch. In all cases, significant growth was observed, and cell densities reached 10⁹ cells/ml. Northern blot analyses revealed different substrate-dependent expression patterns for genes encoding the various endo-acting β-glycosidases; these patterns ranged from strong expression to no expression under the conditions tested. For example, cel74 (TM0305), a gene encoding a putative β-specific endoglucananse, was strongly expressed on all substrates tested, including starch, while no evidence of expression was observed on any substrate for lam16 (TM0024), xyl10A (TM0061), xyl10B (TM0070), and cel12A (TM1524), which are genes that encode a laminarinase, two xylanases, and an endoglucanase, respectively. The cel12B (TM1525) gene, which encodes an endoglucanase, was expressed only on carboxymethyl cellulose. An extracellular mannanase encoded by man5 (TM1227) was expressed on carob galactomannan and konjac glucomannan and to a lesser extent on carboxymethyl cellulose. An unexpected result was the finding that the cel5A (TM1751) and cel5B (TM1752) genes, which encode putative intracellular, β-specific endoglucanases, were induced only when T. maritima was grown on konjac glucomannan. To investigate the biochemical basis of this finding, the recombinant forms of Man5 (M_r, 76,900) and Cel5A (M_r, 37,400) were expressed in Escherichia coli and characterized. Man5, a T. maritima extracellular enzyme, had a melting temperature of 99°C and an optimun temperature of 90°C, compared to 90 and 80°C, respectively, for the intracellular enzyme Cel5A. While Man5 hydrolyzed both galactomannan and glucomannan, no activity was detected on glucans or xylans. Cel5A, however, not only hydrolyzed barley β-glucan, carboxymethyl cellulose, xyloglucan, and lichenin but also had activity comparable to that of Man5 on galactomannan and higher activity than Man5 on glucomannan. The biochemical characteristics of Cel5A, the fact that Cel5A was induced only when T. maritima was grown on glucomannan, and the intracellular localization of Cel5A suggest that the physiological role of this enzyme includes hydrolysis of glucomannan oligosaccharides that are transported following initial hydrolysis by extracellular glycosidases, such as Man5.     

Changes in the photosynthetic efficiency of winter wheat in response to abiotic stress

The assessment of heat and drought tolerance is of primary importance in breeding programmes designed to improve heat and drought tolerance in cereals. Three winter wheat varieties grown in controlled growth chambers were exposed to heat (H) and drought (D) stress singly and in combination (H+D). The combined effects of H and D stress were much more severe than those of individual treatments for both physiological and yield parameters during grain filling. The chlorophyll content, effective quantum yield of PSII, net assimilation rate, transpiration, stomatal conductance and intercellular CO₂ concentration were greatly reduced by H, D and their interaction. Grain yield decreased to a greater extent (48.3%) in Plainsman V, averaged over the stress treatments, than in Mv Magma (67.8%) and Fatima 2 (53.7%). The least decline was found in grain number, except in Plainsman V. Mv Magma tolerated heat stress better than Fatima 2. In terms of photosynthetic activity, Plainsman V showed better drought tolerance than Mv Magma. The results showed that changes in physiological properties during stress treatment are not always associated with changes in yield parameters, so a combination of methods may be needed to give a more precise picture of the stress tolerance of wheat varieties.     

Fusions of the lac operon to the transfer RNA gene tyrT of Escherichia coli.

The tyrT gene codes for one of the tyrosirie tRNA species. Using the Casadabatn (1976a) technique, strains of Escherichia coli were isolated in which the lac structural genes are fused to the promoter of the tyrT gene. This procedure involved obtaining a number of insertions of phage Mu DNA in the tyrT gene, lysogenizing the Mu insertion strains with a λplac-Mu hybrid phage, and selecting Lac⁺ derivatives of such lysogens. In a number of Lac⁺ strains thus obtained, the synthesis of β-galactosidase, the product of the lacZ gene, is regulated in a similar fashion to the synthesis of stable RNA. The fusion strains were shown directly to be tyrT-lac fusions by demonstrating that a Mu insertion in the tyrT gene when genetically recombined into the presumed fusion, inactivates the expression of the lac genes. This result shows that tyrT gene sequences are fused to and control the expression of the lac genes in these strains. This is the first report in which genes which code for proteins have been fused to a stable RNA gene in vivo.     

Gene inactivation in the plant pathogen Glomerella cingulata: three strategies for the disruption of the pectin lyase gene pnIA

The feasibility of performing routine transformation-mediated mutagenesis in Glomerella cingulata was analysed by adopting three one-step gene disruption strategies targeted at the pectin lyase gene pnIA. The efficiencies of disruption following transformation with gene replacement- or gene truncation-disruption vectors were compared. To effect replacement-disruption, G. cingulata was transformed with a vector carrying DNA from the pnlA locus in which the majority of the coding sequence had been replaced by the gene for hygromycin B resistance. Two of the five transformants investigated contained an inactivated pnlA gene (pnlA ^? );both also contained ectopically integrated vector sequences. The efficacy of gene disruption by transformation with two gene truncation-disruption vectors was also assessed. Both vectors carried a 5′and 3′truncated copy of the pnlA coding sequence, adjacent to the gene for hygromycin B resistance. The promoter sequences controlling the selectable marker differed in the two vectors. In one vector the homologous G. cingulata gpdA promoter controlled hygromycin B phosphotransferase expression (homologous truncation vector), whereas in the second vector promoter elements were from the Aspergillus nidulans gpdA gene (heterologous truncation vector). Following transformation with the homologous truncation vector, nine transformants were analysed by Southern hybridisation; no transformants contained a disrupted pnlA gene. Of nineteen heterologous truncation vector transformants, three contained a disrupted pnlA gene; Southern analysis revealed single integrations of vector sequence at pnlA in two of these transformants. pnlA mRNA was not detected by Northern hybridisation in pnlA-transformants. pnlA-transformants failed to produce a PNLA protein with a pI identical to one normally detected in wild-type isolates by silver and activity staining of isoelectric focussing gels. Pathogenesis on Capsicum and apple was unaffected by disruption of the pnlA gene, indicating that the corresponding gene product, PNLA, is not essential for pathogenicity. Gene disruption is a feasible method for selectively mutating defined loci in G. cingulata for functional analysis of the corresponding gene products.