Growth modulation of transgenic potato plants by heterologous expression of bacterial carbohydrate-binding module

Transgenic potato plants (Solanum tuberosum cv. Desiree) expressing the bacterial carbohydrate-binding module (CBM) family III, which is part of the Clostridium cellulovorans CBPA, under control of the CaMV 35S promoter were employed to investigate the influence of this protein on plant development. Eleven independent transgenic plants were found to express the cbm gene, at levels varying from one to four copies. Relative to non-transgenic controls, CBM-expressing plants were characterized by significantly more rapid elongation of the main stem. In addition, under both greenhouse and field conditions, the emergence rate of these plants was higher than in the controls, and their leaf area at early stages of development was larger, resulting in faster accumulation of fresh and dry weight than in control plants. Determination of cell size indicated that epidermal cells in young tissue were significantly larger in CBM-expressing than in control potato plants. These findings suggest that the CBM influence at the cellular level my cause significant alterations in plant growth both in tissue culture and in vivo under field conditions.     

The STE20/germinal center kinase POD6 interacts with the NDR kinase COT1 and is involved in polar tip extension in Neurospora crassa

Members of the Ste20 and NDR protein kinase families are important for normal cell differentiation and morphogenesis in various organisms. We characterized POD6 (NCU02537.2), a novel member of the GCK family of Ste20 kinases that is essential for hyphal tip extension and coordinated branch formation in the filamentous fungus Neurospora crassa. pod-6 and the NDR kinase mutant cot-1 exhibit indistinguishable growth defects, characterized by cessation of cell elongation, hyperbranching, and altered cell-wall composition. We suggest that POD6 and COT1 act in the same genetic pathway, based on the fact that both pod-6 and cot-1 can be suppressed by 1) environmental stresses, 2) altering protein kinase A activity, and 3) common extragenic suppressors (ropy, as well as gul-1, which is characterized here as the ortholog of the budding and fission yeasts SSD1 and Sts5, respectively). Unlinked noncomplementation of cot-1/pod-6 alleles indicates a potential physical interaction between the two kinases, which is further supported by coimmunoprecipitation analyses, partial colocalization of both proteins in wild-type cells, and their common mislocalization in dynein/kinesin mutants. We conclude that POD6 acts together with COT1 and is essential for polar cell extension in a kinesin/dynein-dependent manner in N. crassa.     

Identifying cycling genes by combining sequence homology and expression data

MOTIVATION: The expression of genes during the cell division process has now been studied in many different species. An important goal of these studies is to identify the set of cycling genes. To date, this was done independently for each of the species studied. Due to noise and other data analysis problems, accurately deriving a set of cycling genes from expression data is a hard problem. This is especially true for some of the multicellular organisms, including humans. RESULTS: Here we present the first algorithm that combines microarray expression data from multiple species for identifying cycling genes. Our algorithm represents genes from multiple species as nodes in a graph. Edges between genes represent sequence similarity. Starting with the measured expression values for each species we use Belief Propagation to determine a posterior score for genes. This posterior is used to determine a new set of cycling genes for each species. We applied our algorithm to improve the identification of the set of cell cycle genes in budding yeast and humans. As we show, by incorporating sequence similarity information we were able to obtain a more accurate set of genes compared to methods that rely on expression data alone. Our method was especially successful for the human dataset indicating that it can use a high quality dataset from one species to overcome noise problems in another. AVAILABILITY: C implementation is available from the supporting website: http://www.cs.cmu.edu/~lyongu/pub/cellcycle/.     

Geographic divergence in the relationship between Paragobiodon echinocephalus and its obligate coral host

The redhead goby Paragobiodon echinocephalus lives exclusively within the branching coral Stylophora pistillata . While in the Great Barrier Reef fish occupation rate of large coral is higher than that of small coral, an opposite pattern exists in the northern Red Sea. It is suggested that this pattern is caused by a limitation on the adult body size of fish in the northern Red Sea.     

Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis

The genome sequence of the genetically tractable, mesophilic, hydrogenotrophic methanogen Methanococcus maripaludis contains 1,722 protein-coding genes in a single circular chromosome of 1,661,137 bp. Of the protein-coding genes (open reading frames [ORFs]), 44% were assigned a function, 48% were conserved but had unknown or uncertain functions, and 7.5% (129 ORFs) were unique to M. maripaludis. Of the unique ORFs, 27 were confirmed to encode proteins by the mass spectrometric identification of unique peptides. Genes for most known functions and pathways were identified. For example, a full complement of hydrogenases and methanogenesis enzymes was identified, including eight selenocysteine-containing proteins, with each being paralogous to a cysteine-containing counterpart. At least 59 proteins were predicted to contain iron-sulfur centers, including ferredoxins, polyferredoxins, and subunits of enzymes with various redox functions. Unusual features included the absence of a Cdc6 homolog, implying a variation in replication initiation, and the presence of a bacterial-like RNase HI as well as an RNase HII typical of the Archaea. The presence of alanine dehydrogenase and alanine racemase, which are uniquely present among the Archaea, explained the ability of the organism to use L- and D-alanine as nitrogen sources. Features that contrasted with the related organism Methanocaldococcus jannaschii included the absence of inteins, even though close homologs of most intein-containing proteins were encoded. Although two-thirds of the ORFs had their highest Blastp hits in Methanocaldococcus jannaschii, lateral gene transfer or gene loss has apparently resulted in genes, which are often clustered, with top Blastp hits in more distantly related groups.     

Two biosynthetic pathways for aromatic amino acids in the archaeon Methanococcus maripaludis

Methanococcus maripaludis is a strictly anaerobic, methane-producing archaeon. Aromatic amino acids (AroAAs) are biosynthesized in this autotroph either by the de novo pathway, with chorismate as an intermediate, or by the incorporation of exogenous aryl acids via indolepyruvate oxidoreductase (IOR). In order to evaluate the roles of these pathways, the gene that encodes the third step in the de novo pathway, 3-dehydroquinate dehydratase (DHQ), was deleted. This mutant required all three AroAAs for growth, and no DHQ activity was detectible in cell extracts, compared to 6.0 +/- 0.2 mU mg(-1) in the wild-type extract. The growth requirement for the AroAAs could be fulfilled by the corresponding aryl acids phenylacetate, indoleacetate, and p-hydroxyphenylacetate. The specific incorporation of phenylacetate into phenylalanine by the IOR pathway was demonstrated in vivo by labeling with [1-(13)C]phenylacetate. M. maripaludis has two IOR homologs. A deletion mutant for one of these homologs contained 76, 74, and 42% lower activity for phenylpyruvate, p-hydoxyphenylpyruvate, and indolepyruvate oxidation, respectively, than the wild type. Growth of this mutant in minimal medium was inhibited by the aryl acids, but the AroAAs partially restored growth. Genetic complementation of the IOR mutant also restored much of the wild-type phenotype. Thus, aryl acids appear to regulate the expression or activity of the de novo pathway. The aryl acids did not significantly inhibit the activity of the biosynthetic enzymes chorismate mutase, prephenate dehydratase, and prephenate dehydrogenase in cell extracts, so the inhibition of growth was probably not due to an effect on these enzymes.     

Abnormal `wrinkled' cell walls and retarded development of transgenic Arabidopsis thaliana plants expressing endo-1,4-β-glucanase (cell) antisense

Transgenic Arabidopsis thaliana plants expressing cell antisense exhibit reduced levels of cell mRNA and protein compared with wild-type plants. The former display significant alterations in their phenotype. cell antisense plants have shorter stems and roots and are mechanically weaker than their wild-type counterparts. In cell antisense plants, the cell wall structure is markedly disrupted: both fluorescent confocal microscopy and scanning electron microscopy revealed `wrinkled' cell walls, thus indicating that CEL1 plays an important role in cell wall relaxation during cell growth and expansion. In cell antisense plants, the number of xylem elements per bundle is smaller than in the wild-type. In addition, both xylem elements and interfascicular fibers are significantly less lignified in the former. It is suggested that in A. thaliana, abnormal cell wall deposition affected by CEL1 depletion is associated not only with cell growth, but also with the differentiation process in the vascular and supporting tissues.Equal contributors