Local protein sequence similarity does not imply a structural relationship

A database search often will find a seemingly strong sequence similarity between two fragments of proteins that are not expected to have an evolutionary or functional relationship. It is tempting to suggest that the two fragments will adopt a similar conformation due to a common pattern of residues that dictate a particular substructure. To investigate the likelihood of such a structural similarity, local sequence similarities between proteins of known conformation were identified by a standard database search algorithm. Significant sequence similarity was identified as when the chance probability of obtaining the relatedness score from a scan of the entire database was less than 1%. In this region both true homologies and false homologies are detected. A total of 69 false homologies was located of length between 20 and 262 aligned positions. Many of these alignments had approximately 25% sequence identity and a further 25% of conservative changes. However, the results show in general these aligned fragments did not have a significant similarity in secondary or tertiary structure. Thus local sequence does not indicate a structural similarity when there is neither an evolutionary nor functional explanation to support this. Accordingly structure predictions based on finding a local sequence similarity with an evolutionary unrelated protein of known conformation are unlikely to be valid.     

Embryo rescue response and genetic analyses in interspecific crosses of oilseed Brassica species

Embryo rescue technique is widely utilized to save developing embryo from abortion in interspecific hybridization of plants. In Brassica species, success of an embryo rescue depends on the age of embryo, developmental stage of embryo, and media composition. In this study, ten crosses were conducted between diploid oilseed species B. rapa × tetraploid B. napus and B. rapa × tetraploid B. juncea along with their reciprocal crosses. The immature embryos from parents and crosses were cultured at 14 d after pollination in MS and ½ MS medium without any growth regulators for direct embryogenesis. Embryos were found at different stages of development during isolation, from globular to cotyledonary, indicating that rate of embryo development depends on genotype. Embryos isolated at the cotyledonary stage showed the highest regeneration percentage (av. 83.29%) and required the lowest time to regenerate (5.8 d) compared with another type of embryo, torpedo stage, cultured. Embryo rescued in ½ MS media accounted for 10–51%, 4.0–61%, 6.0–21%, and 5.0–43% greater shoot length, root length, number of leaves, and days to flowering, respectively, in different cross combinations compared with full-strength MS media. The results indicated that the rate of regeneration from embryo is higher in ½ MS media compared with full-strength MS media. Percent regeneration from the cultured embryos differed significantly in different cross combinations. Days required for regeneration from embryos, length of siliqua, and the number of ovules per siliqua accounted for high heterosis and broad sense heritability. The findings of this experiment would be useful in developing cost-effective embryo rescue protocol and desired interspecific hybrids through embryo rescue in Brassica species.

     

Chromosomal localization of human glutathione transferase genes of classes alpha,mu and pi

Summary The numerous human glutathione transferases may be divided into three classes, mu, alpha and pi. Using a panel of human-rodent somatic cell hybrids and DNA probes specific for each of the three classes, we have mapped a class mu gene to chromosome 3, a class alpha gene to chromosome 6 and a class pi gene to chromosome 11. The two latter assignments confirm earlier reports, whereas the assignment of the class mu gene represents a new addition to the human gene map.     

The most frequently lost allelic site in human renal cell carcinoma (D3F15S2) on the short arm of chromosome 3 has homologous sequences on rat chromosome 8

It has previously been shown that human chromosome 3 has banding homology to rat chromosome 8. We have previously isolated a cDNA from the D3F15S2 region and designated the gene as RIK. In the present study, we localized the homolog of this gene to rat chromosome 8.     

Development of fertile fruit bodies in a single-strain culture ofNeurospora crassa

Fertile fruit-bodies (perithecia) were formed in the single-strain culture (EmA) ofNeurospora crassa in the presence of the sex and fertility-inducing substances isolated from the cross EmA x Ema. Analysis of the progeny showed high mortality and an abnormal segregation ratio.     

Interaction between glutamate dehydrogenase (GDH) and L-leucine catabolic enzymes: intersecting metabolic pathways

Branched-chain amino acids (BCAAs) catabolism follows sequential reactions and their metabolites intersect with other metabolic pathways. The initial enzymes in BCAA metabolism, the mitochondrial branched-chain aminotransferase (BCATm), which deaminates the BCAAs to branched-chain α-keto acids (BCKAs); and the branched-chain α-keto acid dehydrogenase enzyme complex (BCKDC), which oxidatively decarboxylates the BCKAs, are organized in a supramolecular complex termed metabolon. Glutamate dehydrogenase (GDH1) is found in the metabolon in rat tissues. Bovine GDH1 binds to the pyridoxamine 5′-phosphate (PMP)-form of human BCATm (PMP-BCATm) but not to pyridoxal 5′-phosphate (PLP)-BCATm in vitro. This protein interaction facilitates reamination of the α-ketoglutarate (αKG) product of the GDH1 oxidative deamination reaction. Human GDH1 appears to act like bovine GDH1 but human GDH2 does not show the same enhancement of BCKDC enzyme activities. Another metabolic enzyme is also found in the metabolon is pyruvate carboxylase (PC). Kinetic results suggest that PC binds to the E1 decarboxylase of BCKDC but does not effect BCAA catabolism. The protein interaction of BCATm and GDH1 promotes regeneration of PLP-BCATm which then binds to BCKDC resulting in channeling of the BCKA products from BCATm first half reaction to E1 and promoting BCAA oxidation and net nitrogen transfer from BCAAs. The cycling of nitrogen through glutamate via the actions of BCATm and GDH1 releases free ammonia. Formation of ammonia may be important for astrocyte glutamine synthesis in the central nervous system. In peripheral tissue association of BCATm and GDH1 would promote BCAA oxidation at physiologically relevant BCAA concentrations.     

<Emphasis Type="Italic">Vibrio cholerae</Emphasis> in waters of the Sunderban mangrove: relationship with biogeochemical parameters and chitin in seston size fractions

Wetland dynamics are probably linked to cholera endemicity in South Asia. We focus on links between Vibrio cholerae abundance, chitin content and suspended particle load in size fractions of suspended particulate matter (SPM) along the salinity gradient of Sunderban mangrove waters. SPM decreased downstream, while salinity increased from 0.2 to 4. Particulate organic carbon (90 ± 25 μM) and nitrogen (9.1 ± 3.3 μM) highly correlated with SPM and turbidity, suggesting a significant contribution of fine particles to organic matter. Total chitin ranged 1–2 mg/l and decreased downstream. The distribution among size fractions of SPM, chitin and V. cholerae O1 (the bacterial serogroup mainly associated with cholera epidemics) was similar, with ~98% of the total in the fraction <20 μm. In comparison, the number of V. cholerae O1 attached to zooplankton and microplankton size classes >20 μm was almost negligible, in contrast to usual assumptions. Thus, microdetritus, nanoplankton and fungal cells in size classes <20 μm represent a chitinaceous substrate on which V. cholerae can grow and survive. Total bacteria, cultivable vibrios and V. cholera O1 increased 5–10 times downstream, together with salinity and nitrite concentration. Overall, nitrate and silicate concentrations were relatively constant (>22 μM N and 100 μM Si). However, nitrite increased ~9 times in the outer sector, reaching ~1.2 μM N, probably as a result of increased abundance of nitrate-reducing vibrios. A characterization of Vibrio habitats that takes account of the presence of nitrate-reducing bacteria could improve the understanding of both mangrove nitrogen cycling and cholera seasonality.