Annotating gene function by combining expression data with a modular gene network

MOTIVATION: A promising and reliable approach to annotate gene function is clustering genes not only by using gene expression data but also literature information, especially gene networks. RESULTS: We present a systematic method for gene clustering by combining these totally different two types of data, particularly focusing on network modularity, a global feature of gene networks. Our method is based on learning a probabilistic model, which we call a hidden modular random field in which the relation between hidden variables directly represents a given gene network. Our learning algorithm which minimizes an energy function considering the network modularity is practically time-efficient, regardless of using the global network property. We evaluated our method by using a metabolic network and microarray expression data, changing with microarray datasets, parameters of our model and gold standard clusters. Experimental results showed that our method outperformed other four competing methods, including k-means and existing graph partitioning methods, being statistically significant in all cases. Further detailed analysis showed that our method could group a set of genes into a cluster which corresponds to the folate metabolic pathway while other methods could not. From these results, we can say that our method is highly effective for gene clustering and annotating gene function.     

Termite soldier differentiation in incipient colonies is related to parental proctodeal trophallactic behavior

Termite soldiers represent a peculiar caste among social insects in terms of their specific defensive roles. Numbers of soldiers are relatively low in a mature colony, and it is impossible to identify the individuals that will differentiate into soldiers. If it were possible to specify these individuals prior to soldier differentiation, it would facilitate a better understanding of the regulatory mechanisms of soldier differentiation under natural condition. Here we analyzed soldier differentiation in incipient colonies of Zootermopsis nevadensis, in which only a single soldier develops via a presoldier stage, and is stable during early colony ontogeny. We observed that the oldest third instar differentiated into a presoldier within about eight days from its appearance. Caste differentiation, however, was not strictly determined on an individual basis. The oldest third instars never differentiated into presoldiers if primary reproductives were removed soon after their appearance. Behavioral observations of primary reproductives and their offspring prior to presoldier differentiation, showed that primary reproductives transferred proctodeal materials to the oldest third instar significantly more frequently than to other larva. A high juvenile hormone (JH) titer is required for the soldier differentiation, and we suggest that the JH itself or some nutrients/factors increasing larval JH titer may be transferred to the oldest third instar via a parental proctodeal fluid.     

Effect of photoperiod on clock gene expression and subcellular distribution of PERIOD in the circadian clock neurons of the blow fly Protophormia terraenovae

We examined the effect of photoperiod on the expression of circadian clock genes period (per) and timeless (tim), using quantitative real-time polymerase chain reaction (PCR), and the effect of photoperiod on subcellular distribution of PERIOD (PER), using immunocytochemistry, in the blow fly, Protophormia terraenovae. Under both short-day and long-day conditions, the mRNA levels of per and tim in the brain oscillated, and their peaks and troughs occurred around lights-off and lights-on, respectively. The oscillations persisted even under constant darkness. In the large ventral lateral neurons (l-LN_vs), small ventral lateral neurons (s-LN_vs), dorsal lateral neurons (LN_ds), and medial dorsal neurons (DN_ms), the subcellular distribution of PER-immunoreactivity changed with time. The number of cells with PER-immunoreactivity in the nucleus was highest 12 h after lights-off and lowest 12 h after lights-on, regardless of photoperiod, suggesting that PER nuclear translocation entrains to photoperiod. When temporal changes in the nuclear localization of PER were compared, the neurons could be classified into 2 groups: the l-LN_vs were similar to the s-LN_vs, and the LN_ds were similar to DN_ms. In LN_ds and DN_ms, decreasing rates of the number of cells with PER immunoreactivity in the nucleus per brain from the maximum were large as compared with those in l-LN_vs and s-LN_vs under short-day conditions. These results suggest that photoperiodic information is reflected in the expression patterns of circadian clock genes per and tim and in the subcellular distribution of PER. This observation suggests that the 2 different groups of clock neurons respond to photoperiod in slightly different manners.     

Structure of the transition state analog of medium-chain acyl-CoA dehydrogenase. Crystallographic and molecular orbital studies on the charge-transfer complex of medium-chain acyl-CoA dehydrogenase with 3-thiaoctanoyl-CoA

The flavoenzyme medium-chain acyl-CoA dehydrogenase (MCAD) eliminates the alpha-proton of the substrate analog, 3-thiaoctanoyl-CoA (3S-C8-CoA), to form a charge-transfer complex with deprotonated 3S-C8-CoA. This complex can simulate the metastable reaction intermediate immediately after the alpha-proton elimination of a substrate and before the beta-hydrogen transfer as a hydride, and is therefore regarded as a transition-state analog. The crystalline complex was obtained by co-crystallizing MCAD in the oxidized form with 3S-C8-CoA. The three-dimensional structure of the complex was solved by X-ray crystallography. The deprotonated 3S-C8-CoA was clearly located within the active-site cleft of the enzyme. The arrangement between the flavin ring and deprotonated 3S-C8-CoA is consistent with a charge transfer interaction with the negatively charged acyl-chain of 3S-C8-CoA as an electron donor stacking on the pyrimidine moiety of the flavin ring as an electron acceptor. The structure of the model complex between lumiflavin and the deprotonated ethylthioester of 3-thiabutanoic acid was optimized by molecular orbital calculations. The obtained theoretical structure was essentially the same as that of the corresponding region of the X-ray structure. A considerable amount of negative charge is transferred to the flavin ring system to stabilize the complex by 9.2 kcal/mol. The large stabilization energy by charge transfer probably plays an important role in determining the alignment of the flavin ring with 3S-C8-CoA. The structure of the highest occupied molecular orbital of the complex revealed the electron flow pathway from a substrate to the flavin ring.     

Characterization of the transmembrane channel-like (TMC) gene family: functional clues from hearing loss and epidermodysplasia verruciformis

Mutations of TMC1 cause deafness in humans and mice. TMC1 and a related gene, TMC2, are the founding members of a novel gene family. Here we describe six additional TMC paralogs (TMC3 to TMC8) in humans and mice, as well as homologs in other species. cDNAs spanning the full length of the predicted open reading frames of the mammalian genes were cloned and sequenced. All are strongly predicted to encode proteins with 6 to 10 transmembrane domains and a novel conserved 120-amino-acid sequence that we termed the TMC domain. TMC1, TMC2, and TMC3 comprise a distinct subfamily expressed at low levels, whereas TMC4 to TMC8 are expressed at higher levels in multiple tissues. TMC6 and TMC8 are identical to the EVER1 and EVER2 genes implicated in epidermodysplasia verruciformis, a recessive disorder comprising susceptibility to cutaneous human papilloma virus infections and associated nonmelanoma skin cancers, providing additional genetic and tissue systems in which to study the TMC gene family.     

APAF-1-ALT,a novel alternative splicing form of APAF-1, potentially causes impeded ability of undergoing DNA damage-induced apoptosis in the LNCaP human prostate cancer cell line

We have found a novel alternative splicing product of the apoptotic protease activating factor 1 (APAF-1), termed APAF-1-ALT, in the LNCaP human prostate cancer cell line. APAF-1-ALT harbors the caspase recruitment domain and an incomplete CED-4 like/ATPase domain, but lacks the WD-40 repeat units. The LNCaP cell expressed the full-length APAF-1 weakly and APAF-1-ALT rather abundantly, especially after mycoplasma infection. LNCaP underwent a retarded DNA damage-induced apoptosis, which was independent of caspase 9 activity. APAF-1-ALT functioned less effectively in inducing apoptosis than did APAF-1-XL, the full-length APAF-1, in transient transfection. Moreover, APAF-1-ALT interfered with APAF-1-XL's ability to induce apoptosis in transient double transfection experiment. These results indicate that APAF-1-ALT is a molecule that is deficient and impeded for mediating apoptosis and that it may contribute to the resistance to DNA damage-induced treatment observed in LNCaP.     

Biogeography of Japanese wood-feeding cockroaches genus Salganea and Panesthia (Blaberidae: Panesthiinae)

We investigated mitochondrial COII gene sequences of Japanese wood-feeding cockroaches (Salganea spp. and Panesthia angustipennis) in detail to investigate their biogeography. The transition (TI) numbers between each genus north and south of the Tokara Strait, which is a border of the Oriental and the Palaearctic faunal regions, were almost same, but the transversion (TV) numbers were much lower in Panesthia compared with Salganea. These tendencies suggest that multiple substitutions of TIs occurred between certain pairs of Salganea taxa and that the genera must have entered to the north of the Tokara Strait at different times. Phylogenetic relationships and estimated divergence times using TVs divergences suggest that Salganea species and Panesthia taxa north and south of the Tokara Strait were diverged from each other during the latter half of the Miocene and from the late Pliocene to the early Pleistocene, respectively. These two periods are nearly consistent with the two land expanding times in the Ryukyu Islands supported by the recent palaeogeographical hypotheses.     

BRYOPSIS MAXIMA (CHLOROPHYTA) GLUTAMATE DEHYDROGENASE: MULTIPLE GENES AND ISOZYMES

Subcellular localization of glutamate dehydrogenase (GDH) was investigated in the green alga Bryopsis maxima. Both intact and pure chloroplasts and mitochondria were isolated by two methods: successive centrifugation and continuous Percoll density gradient centrifugation. The NADP-dependent GDH activities of the chloroplastic, mitochondrial, and cytosolic portions were estimated as 64.3, 9.8, and 25.9%, respectively, and NAD-dependent GDH activity was observed only in the chloroplasts. Three organelle-specific isozymes—chloroplastic NADP-GDH1, cytosolic/mitochondrial NADP-GDH2, and cytosolic/mitochondrial NADP-GDH3—were purified. The molecular masses of these isozymes were estimated to be the same (280 kDa). K_m values of NADP-GDH1, NADP-GDH2, and NADP-GDH3 for NADPH in the amination reaction were 30, 110, and 34 μM, respectively, and those for NADH were 185, 1490, and 974 μM, respectively, showing different cofactor affinities. Several NADP-GDHs and one NAD-GDH were induced in the chloroplasts during incubation of the collected thalli in either continuous light or darkness in aerated seawater for 0 to 5 days, whereas the cytosolic and mitochondrial NADP-GDHs decreased to an almost undetectable level in 5 days. Two distinct DNA fragments (BmF-1 and BmF-2) encoding B. maxima Okamura GDH were identified and sequenced. They showed 90% homology in their deduced amino acid sequences, whereas synonymous nucleotide substitution was observed in the third position of 52% of the codons. Genomic Southern analysis suggested that the two genes are located at two different loci on the B. maxima chromosome. Thus, B. maxima GDH has been confirmed to be multiple in terms of both protein and gene. The localization of other nitrogen-assimilating enzymes was also determined. Glutamine synthetase was located in the chloroplasts and the cytosol, glutamate synthase was located in the chloroplasts, and nitrate reductase was located in the cytosol.     

Resonance Raman study on the flavin in the purple intermediates of D-amino acid oxidase

Resonance Raman (RR) spectra were measured for the purple intermediates of D-amino acid oxidase reconstituted with isotopically labelled FAD's, i.e., [4a-13C]-, [4,10a-13C2]-, [2-13C]-, [5-15N]-, and [1,3-15N2]flavin adenine dinucleotides, and compared with those with the native enzyme. The RR lines around 1605 cm-1 with D-alanine or D-proline as a substrate and at 1548 cm-1 with D-alanine undergo isotopic shifts upon [4a-13C]- and [4,10a-13C2]-labelling. These lines are assigned to the vibrational modes associated with C(10a) = C(4a) - C(4) = O moiety of reduced flavin, providing the first assignment of RR lines of reduced flavin and conclusive evidence that reduced flavin is involved in this intermediate.