Cloning of ndhK from soybean chloroplasts using antibodies raised to mitochondrial complex I

DLX6-AS1 is a potential biomarker and therapeutic target in cancer initiation and progression

Long noncoding RNAs (lncRNAs) are involved in multiple functions such as the regulation of cellular homeostasis. They play prominent roles in the pathogenesis of human cancer, and contribute to every hallmark of cancer. The novel cancer-related lncRNA DLX6 antisense RNA 1 (DLX6-AS1) plays an essential regulatory role in enhancing and initiating carcinogenesis and tumor progression. This progression is due to the aberrant regulation of downstream factors in vitro as well as in vivo. DLX6-AS1 is significantly dysregulated in various cancers. DLX6-AS1 functions in tumor initiation and progression are regulated at the epigenetic, transcription, and posttranscriptional regulation levels. DLX6-AS1 functions as an oncogene, binding to miRNA targeting sites competing endogenous RNAs and causing the upregulation of downstream tumor-related genes and carcinogenesis. The regulation and detailed molecular mechanisms of DLX6-AS1 and its potential role in malignancies are comprehensively described in this paper. DLX6-AS1 has the potential to become a novel biomarker and therapeutic target for cancer.

Comparative analysis of complete chloroplast genome sequences of four major Amorphophallus species

Amorphophallus (Araceae) contains more than 170 species that are mainly distributed in Asia and Africa. Because the bulbs of Amorphophallus are rich in glucomannan, they have been widely used in food, medicine, the chemical industry and so on. To better understand the evolutionary relationships and mutation patterns in the chloroplast genome of Amorphophallus, the complete chloroplast genomes of four species were sequenced. The chloroplast genome sequences of A. albus, A. bulbifer, A. konjac and A. muelleri ranged from 162,853 bp to 167,424 bp. The A. albus chloroplast (cp) genome contains 113 genes, including 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes. The A. bulbifer cp genome contains 111 genes, including 78 protein-coding genes, 29 tRNA genes and 4 rRNA genes. A. muelleri contains 111 and 113 genes, comprising 78 and 80 protein-coding genes, respectively, 29 tRNA genes and 4 rRNA genes. The IR (inverted repeat) region/LSC (long single copy) region and IR/SSC (short single copy) region borders of the four Amorphophallus cp genomes were compared. In addition to some genes being deleted, variations in the copy numbers and intron numbers existed in some genes in the four cp genomes. One hundred thirty-four to 164 SSRs (simple sequence repeats) were detected in the four cp genomes. In addition, the highest mononucleotide SSRs were composed of A and T repeat units, and the majority of dinucleotides were composed of AT and TA. SNPs (single nucleotide polymorphisms) and indels (insertion-deletions) were calculated from coding genes and noncoding genes, respectively. These divergences comprising SSRs, SNPs and indel markers will be useful in testing the maternal inheritance of the chloroplast genome, identifying species differentiation and even in breeding programs. Furthermore, the regression of ndhK was detected from four Amorphophallus cp genomes in our study. Complete cp genome sequences of four Amorphophallus species and other plants were used to perform phylogenetic analyses. The results showed that Amorphophallus was clustered in Araceae, and Amorphophallus was divided into two clades; A. albus and A. konjac were clustered in one clade, and A. bulbifer and A. muelleri were clustered in another clade. Phylogenetic analysis among the Amorphophallus genus was conducted based on matK and rbcL. The phylogenetic trees showed that the relationships among the Amorphophallus species were consistent with their geographical locations. The complete chloroplast genome sequence information for the four Amorphophallus species will be helpful for elucidating Amorphophallus phylogenetic relationships.

Termination codon-dependent translation of partially overlapping ndhC-ndhK transcripts in chloroplasts

The chloroplast NAD(P)H dehydrogenase complex, a homologue of mitochondrial complex I, consists of >15 subunits, of which 11 are encoded by the chloroplast genome (ndhA-K). The ndhC and ndhK genes are partially overlapped and cotranscribed in many land plants. The downstream ndhK mRNA possesses 4 possible AUG initiation codons in many dicot plants. By using an efficient in vitro translation system from tobacco chloroplasts, we defined that the major initiation site of tobacco ndhK mRNAs is the third AUG that is located 4 nt upstream from the ndhC stop codon. Mutation of the ndhC stop codon (UAG) arrested translation of the ndhK cistron. Frameshift of the ndhC coding strand inhibited also translation of the distal cistron. The results indicated that ndhK translation depends on termination of the preceding cistron, namely translational coupling. Surprisingly, removal of the ndhC 5'-UTR and its AUG still supported substantial translation of the ndhK cistron. This translation was abolished again by removing the ndhC stop codon. Although translation of the downstream cistron of an overlapping mRNA is generally very low, we found that the ndhC/K mRNA produces NdhK and NdhC in similar amounts. Based on subunit compositions of the bacterial complex I, the stoichiometry of NdhK and NdhC is suggested to be 1:1 in chloroplasts. To meet this stoichiometry, the ndhC/K mRNA is translated not only by a translational coupling event but also by a termination codon-dependent pathway.

Chlororespiration

Chlororespiration has been defined as a respiratory electron transport chain (ETC) in interaction with the photosynthetic ETC in thylakoid membranes of chloroplasts. The existence of chlororespiration has been disputed during the last decade, with the initial evidence mainly obtained with intact algal cells being possibly explained by redox interactions between chloroplasts and mitochondria. The discovery in higher-plant chloroplasts of a plastid-encoded NAD(P)H-dehydrogenase (Ndh) complex, homologous to the bacterial complex I, and of a nuclear-encoded plastid terminal oxidase (PTOX), homologous to the plant mitochondrial alternative oxidase, brought molecular support to the concept of chlororespiration. The functionality of these proteins in non-photochemical reduction and oxidation of plastoquinones (PQs), respectively, has recently been demonstrated. In thylakoids of mature chloroplasts, chlororespiration appears to be a relatively minor pathway compared to linear photosynthetic electron flow from H2O to NADP+. However, chlororespiration might play a role in the regulation of photosynthesis by modulating the activity of cyclic electron flow around photosystem I (PS I). In non-photosynthetic plastids, chlororespiratory electron carriers are more abundant and may play a significant bioenergetic role.

Reduction of the plastoquinone pool by exogenous NADH and NADPH in higher plant chloroplasts. Characterization of a NAD(P)H-plastoquinone oxidoreductase activity

Chlorophyll fluorescence measurements were performed on osmotically lysed potato chloroplasts in order to characterize the reactions involved in the dark reduction of photosynthetic inter-system chain electron carriers. Addition of NADH or NADPH to lysed chloroplasts increased the chlorophyll fluorescence level measured in the presence of a non-actinic light until reaching Fmax, thus indicating an increase in the redox state of the plastoquinone (PQ) pool. The fluorescence increase was more pronounced when the experiment was carried out under anaerobic conditions and was about 50% higher when NADH rather than NADPH was used as an electron donor. The NAD(P)H-PQ oxidoreductase reaction was inhibited by diphenylene iodonium, N-ethylmaleimide and dicoumarol, but insensitive to rotenone, antimycin A and piericidin A. By comparing the substrate specificity and the inhibitor sensitivity of this reaction to the properties of spinach ferredoxin-NADP+-reductase (FNR), we infer that FNR is not involved in the NAD(P)H-PQ oxidoreductase activity and conclude to the participation of rotenone-insensitive NAD(P)H-PQ oxidoreductase. By measuring light-dependent oxygen uptake in the presence of DCMU, methyl viologen and NADH or NADPH as an electron donors, the electron flow rate through the NAD(P)H-PQ oxidoreductase is estimated to about 160 nmol O2 min-1 mg-1 chlorophyll. The nature of this enzyme is discussed in relation to the existence of a thylakoidal NADH dehydrogenase complex encoded by plastidial ndh genes. Copyright 1998 Elsevier Science B.V.

The plant mitochondrial 22 kDa (PSST) subunit of respiratory chain complex I is encoded by a nuclear gene with enhanced transcript levels in flowers

Genes for subunits of respiratory chain complex I are found in mitochondrial, plastid and/or nuclear genomes with varying distributions in the diverse eukaryotic species. The intrinsic PSST subunit of complex I is a mitochondrially encoded protein in Paramecium but is specified by a nuclear gene in animals. In plants to date only the homologous plastid encoded NDH-K gene product has been described. The analogous plant mitochondrial protein is now identified as the 22 kDa complex I subunit and found to be encoded in the nuclear genome of Arabidopsis and potato. The cDNA sequences of clones isolated from both plants are 79% identical in the conserved coding region, while the 5' parts of the reading frames specifying the N-terminal presequences for mitochondrial import differ significantly. The expression of the genes examined in different organs of both plants by Northern blot analysis shows elevated steady-state mRNA levels in flowers. Hence, expression of the gene appears to be organ-specifically regulated by its transcription rate and/or mRNA stability. A 1.6 kb long genomic DNA sequence of Arabidopsis upstream of the transcribed gene region encoding the PSST subunit in Arabidopsis contains several putative promoter sequence motifs. The results are discussed with regard to the appearance of a nuclearly integrated, former mitochondrial gene.

Cloning, analysis and inactivation of the ndhK gene encoding a subunit of NADH quinone oxidoreductase from Anabaena PCC 7120

The function of the type-1 pyridine nucleotide dehydrogenase (NDH-1) in the cyanobacterium Anabaena PCC 7120 was investigated. Immunological analysis with antibodies raised against NdhK from Synechocystis PCC 6803, a subunit of NDH-1, showed that NdhK in Anabaena PCC 7120 is only present on the plasma membrane, which confirms the results of previous studies [Howitt, C.A., Smith, G.D. & Day, D. A. (1993) Biochim. Biophys. Acta 114], 313-320]. Southern analysis with probes from the operon encoding ndhC-K-J from Synechocystis PCC 6803 showed that this operon is also conserved in Anabaena PCC 7120. Part of the operon was amplified using PCR with degenerate primers designed against two sequences encoding regions of NdhC and NdhJ that are conserved between cyanobacteria and chloroplasts. The nucleotide sequence of ndhK encodes a protein of 245 amino acids with a predicted molecular mass of 27.5 kDa. The coding regions of ndhC and ndhK overlap by 7 bp, as found in the chloroplasts of liverwort, maize, and rice. This is markedly different from the case in Synechocystis PCC 6803 where a 71-bp non-coding, intergenic spacer region lies between ndhC and ndhK. The ndhK clone was interrupted by the insertion of a kanamycin-resistance gene and used to transform Anabaena PCC 7120.20 unsegregated transformants were produced, all of which died during attempts to segregate them. This indicates that under the selection conditions used, ndhK is an essential gene in Anabaena PCC 7120.

Kinetic and functional characterization of a membrane-bound NAD(P)H dehydrogenase located in the chloroplasts of Pleurochloris meiringensis (Xanthophyceae)

Using isolated chloroplasts or purified thylakoids from photoautotrophically grown cells of the chromophytic alga Pleurochloris meiringensis (Xanthophyceae) we were able to demonstrate a membrane bound NAD(P)H dehydrogenase activity. NAD(P)H oxidation was detectable with menadione, coenzyme Q0, decylplastoquinone and decylubiquinone as acceptors in an in vitro assay. K m-values for both pyridine nucleotides were in the μmolar range (K m[NADH]=9.8 μM, K m[NADPH]=3.2 μM calculated according to Lineweaver-Burk). NADH oxidation was optimal at pH 9 while pH dependence of NADPH oxidation showed a main peak at 9.8 and a smaller optimum at pH 7.5-8. NADH oxidation could be completely inhibited with rotenone, an inhibitor of mitochondrial complex I dehydrogenase, while NADPH oxidation revealed the typical inhibition pattern upon addition of oxidized pyridine nucleotides reported for ferredoxin: NADP(+) reductase. Partly-denaturing gel electrophoresis followed by NAD(P)H dehydrogenase activity staining showed that NADPH and NADH oxidizing proteins had different electrophoretic mobilities. As revealed by denaturing electrophoresis, the NADH oxidizing enzyme had one main subunit of 22 kDa and two further polypeptides of 29 and 44 kDa, whereas separation of the NADPH depending protein yielded five bands of different molecular weight. Measurement of oxygen consumption due to PS I mediated methylviologen reduction upon complete inhibition of PS II showed that the NAD(P)H dehydrogenase is able to catalyze an input of electrons from NADH to the photosynthetic electron transport chain in case of an oxidized plastoquinone-pool. We suggest ferredoxin: NADP(+) reductase to be the main NADPH oxidizing activity while a thylakoidal NAD(P)H: plastoquinone oxidoreductase involved in the chlororespiratory pathway in the dark acts mainly as an NADH oxidizing enzyme.

Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii

The complete nucleotide sequence (119,707 bp) of the black pine (Pinus thunbergii) chloroplast genome has been determined. It contains 4 rRNA genes and 32 tRNA genes. To our knowledge, the tRNAPro (GGG) gene has not been found in any other chloroplast genome analyzed. Sixty-one genes encoding proteins and 11 conserved open reading frames are also found. Extensive rearrangements are apparent in the chloroplast genome relative to those of other land plants. The most striking feature is the loss of all 11 functional genes (ndh genes) for subunits of a putative NADH dehydrogenase that are found in the chloroplast genomes of angiosperms and a bryophyte. Four ndh genes were completely lost and the other 7 genes remain as obvious pseudogenes. This unexpected finding raises the possibility that all ndh genes have been transferred to the nucleus or that an NADH dehydrogenase is not essential in black pine chloroplasts.

Functional loss of all ndh genes in an otherwise relatively unaltered plastid genome of the holoparasitic flowering plant Cuscuta reflexa

We have cloned and sequenced an area of about 9.0 kb of the plastid DNA (ptDNA) from the holoparasitic flowering plant Cuscuta reflexa to investigate the evolutionary response of plastid genes to a reduced selective pressure. The region contains genes for the 16S rRNA, a subunit of a plastid NAD(P)H dehydrogenase (ndhB), three transfer RNAs (trnA, trnI, trnV) as well as the gene coding for the ribosomal protein S7 (rps7). While the other genes are strongly conserved in C. reflexa, the ndhB gene is a pseudogene due to many frameshift mutations. In addition we used heterologous gene probes to identify the other ndh genes encoded by the plastid genome in higher plants. No hybridization signals could be obtained, suggesting that these genes are either lost or strongly altered in the ptDNA of C. reflexa. Together with evidence of deleted genes in the ptDNA of C. reflexa, the plastid genome can be grouped into four classes reflecting a different evolutionary rate in each case. The phylogenetic position of Cuscuta and the significance of ndh genes in the plastid genome of higher plants are discussed.