Mitochondrial Transcription Termination Factor Research Articles

Arabidopsis mTERF9 protein promotes chloroplast ribosomal assembly and translation by establishing ribonucleoprotein interactions in vivo.

The mitochondrial transcription termination factor proteins are nuclear-encoded nucleic acid binders defined by degenerate tandem helical-repeats of ∼30 amino acids. They are found in metazoans and plants where they localize in organelles. In higher plants, the mTERF family comprises ∼30 members and several of these have been linked to plant development and response to abiotic stress. However, knowledge of the molecular basis underlying these physiological effects is scarce. We show that the Arabidopsis mTERF9 protein promotes the accumulation of the 16S and 23S rRNAs in chloroplasts, and interacts predominantly with the 16S rRNA in vivo and in vitro. Furthermore, mTERF9 is found in large complexes containing ribosomes and polysomes in chloroplasts. The comprehensive analysis of mTERF9 in vivo protein interactome identified many subunits of the 70S ribosome whose assembly is compromised in the null mterf9 mutant, putative ribosome biogenesis factors and CPN60 chaperonins. Protein interaction assays in yeast revealed that mTERF9 directly interact with these proteins. Our data demonstrate that mTERF9 integrates protein-protein and protein-RNA interactions to promote chloroplast ribosomal assembly and translation. Besides extending our knowledge of mTERF functional repertoire in plants, these findings provide an important insight into the chloroplast ribosome biogenesis.

Arabidopsis Seedling Lethal 1 Interacting With Plastid-Encoded RNA Polymerase Complex Proteins Is Essential for Chloroplast Development.

Mitochondrial transcription termination factors (mTERFs) are highly conserved proteins in metazoans. Plants have many more mTERF proteins than animals. The functions and the underlying mechanisms of plants’ mTERFs remain largely unknown. In plants, mTERF family proteins are present in both mitochondria and plastids and are involved in gene expression in these organelles through different mechanisms. In this study, we screened Arabidopsis mutants with pigment-defective phenotypes and isolated a T-DNA insertion mutant exhibiting seedling-lethal and albino phenotypes [seedling lethal 1 (sl1)]. The SL1 gene encodes an mTERF protein localized in the chloroplast stroma. The sl1 mutant showed severe defects in chloroplast development, photosystem assembly, and the accumulation of photosynthetic proteins. Furthermore, the transcript levels of some plastid-encoded proteins were significantly reduced in the mutant, suggesting that SL1/mTERF3 may function in the chloroplast gene expression. Indeed, SL1/mTERF3 interacted with PAP12/PTAC7, PAP5/PTAC12, and PAP7/PTAC14 in the subgroup of DNA/RNA metabolism in the plastid-encoded RNA polymerase (PEP) complex. Taken together, the characterization of the plant chloroplast mTERF protein, SL1/mTERF3, that associated with PEP complex proteins provided new insights into RNA transcription in the chloroplast.

Identification of Rf9, a Gene Contributing to the Genetic Complexity of Fertility Restoration in Hybrid Wheat.

Wheat (Triticum aestivum L.) is a self-pollinating crop whose hybrids offer the potential to provide a major boost in yield. Male sterility induced by the cytoplasm of Triticum timopheevii is a powerful method for hybrid seed production. Hybrids produced by this method are often partially sterile, and full fertility restoration is crucial for wheat production using hybrid cultivars. To identify the genetic loci controlling fertility restoration in wheat, we produced two cytoplasmic male-sterile (CMS) backcross (BC1) mapping populations. The restorer lines Gerek 79 and 71R1203 were used to pollinate the male-sterile winter wheat line CMS-Sperber. Seed set and numbers of sterile spikelets per spike were evaluated in 340 and 206 individuals of the populations derived from Gerek 79 and 71R1203, respectively. Genetic maps were constructed using 930 and 994 single nucleotide polymorphism (SNP) markers, spanning 2,160 and 2,328 cM over 21 linkage groups in the two populations, respectively. Twelve quantitative trait loci (QTL) controlled fertility restoration in both BC1 populations, including a novel restorer-of-fertility (Rf) locus flanked by the SNP markers IWB72413 and IWB1550 on chromosome 6AS. The locus was mapped as a qualitative trait in the BC1 Gerek 79 population and was designated Rf9. One hundred-nineteen putative candidate genes were predicted within the QTL region on chromosome 6AS. Among them were genes encoding mitochondrial transcription termination factor and pentatricopeptide repeat-containing proteins that are known to be associated with fertility restoration. This finding is a promising step to better understand the functions of genes for improving fertility restoration in hybrid wheat.

Characterization of Transcriptome Expression: The Response of Isatis indigotica to Salt Stress

Isatis indigotica Fort. is extremely widely planted and used for the source of the traditional Chinese medicine Radix Isatidis (Ban-Lan-Gen), which had pharmacological activities such as anti-endotoxic, antibacterial, antinociceptive, anti-inflammatory and antipyretic. In the cultivation, salt stress could affect the yields of Radix Isatidis, and activate the secondary metabolism, eg. the contents of epigoitrin in root and indigo in leaf increased after a period of salt stress, which was possibly regulated by related genes. But in early salt stress, the molecular response of I. indigotica and expression of related genes are also worthy of our attention, which it helps us to more fully understand the molecular response mechanism of I. indigotica, so that we can make better use of “salt stress” to stimulate its secondary metabolism. To determine the molecular changes of I. indigotica in salt stress, the RNA-seq was carried out for the expression profile with NGS QC Toolkit (v2.3.2) software, the Illumina HiSeqTM 2000 in Biomarker Technologies Co., Ltd and ESTScan program. The de novo assembly resulted in 33109 unigenes from more than 18.71 Gb data. Of these, 28868 unigenes were annotated using KOG, KEGG, Nr, Nt, Swiss-Prot and TrEMBL databases. Then, 11829 simple sequence repeats were found in unigenes and 7725 primers were designed. After detecting the expression value, the edgeR package found 135 DEG, of those 48 were up-regulated and 87 were down-regulated. The expression pattern of genes that was validated by qPCR indicated that mitochondrial transcription termination factor, non-LTR retroelement reverse transcriptase and CYP79F1 which involved in the first step in biosynthesis of core short-chain aliphatic glucosinolates might play a vital role in coping with salt stress. Although one assembly of I. indigotica unigenes were obtained before, this study would provide more molecular data for further analysis, and facilitate studies on the functions of genes involved in the salt related signal pathways.

The Molecular Function of Plant mTERFs as Key Regulators of Organellar Gene Expression.

The protein family of mTERFs (mitochondrial transcription termination factors) was initially studied in mammalian and insect mitochondria before the first Arabidopsis mTERF mutant was characterized. More than 10 years of research on the function of plant mTERFs in the flowering plants Arabidopsis thaliana, Zea mays and the green microalga Chlamydomonas reinhardtii has since highlighted that mTERFs are key regulators of organellar gene expression (OGE) in mitochondria and in chloroplasts. Additional functions to be fulfilled by plant mTERFs (e.g. splicing) and the fact that the expression of two organellar genomes had to be facilitated have led to a massive expansion of the plant mTERF portfolio compared to that found in mammals. Plant mTERFs are implicated in all steps of OGE ranging from the modulation of transcription to the maturation of tRNAs and hence translation. Furthermore, being regulators of OGE, mTERFs are required for a successful long-term acclimation to abiotic stress, retrograde signaling and interorganellar communication. Here, I review the recent progress in the elucidation of molecular mTERF functions.

Abstract B67: Genome-wide 5-hydroxymethylcytosine mapping in circulating cell-free DNA reveals prognostic implications in pancreatic ductal adenocarcinoma

Abstract Pancreatic ductal adenocarcinoma (PDAC) is only the 11th most common cancer globally, but PDAC comprises a disproportionate number of total cancer deaths, ranking 7th worldwide for cancer mortality with over 400,000 annual deaths. Although advances in cancer research and clinical oncology have significantly improved patient outcomes for many human cancers, the prognosis of PDAC remains dismal with a ~5% survival rate five years after diagnosis. Precise prognosis for PDAC will likely improve clinical outcomes, e.g., through evidence-based selection of the best treatment options. Our team demonstrated the diagnostic value of 5-hydroxymethylcytosines (5hmC), a novel epigenetic marker that has been implicated in cancer pathobiology, in circulating cell-free DNA (cfDNA) for PDAC (Zhang et al., 2019 AACR Annual Meeting). In this study, we sought to explore the prognostic implications of 5hmC in cfDNA for PDAC as a minimally invasive approach. Specifically, we prospectively recruited 56 patients with PDAC (age: 60.91 ± 9.68; males: 50%) from Peking Union Medical College Hospital. We excluded patients treated with chemotherapy, radiation therapy, or immunotherapy and obtained baseline clinical, laboratory, and treatment data. Tumor staging was based on the Cancer Staging Manual (8th edition) from the American Joint Committee on Cancer. We performed genome-wide 5hmC mapping in patient-derived cfDNA using the 5hmC-Seal technique, a highly sensitive method requiring < 5 mL of plasma. We evaluated the potential prognostic value of the 5hmC in cfDNA for predicting overall survival (all-cause mortality) within 36 months after surgery. We detected a panel of 12 marker genes using the elastic net regularization on the Cox proportional hazards model and developed a weighted prognostic score. The 5hmC-based prognostic scores separated patients by their overall survival (Hazard Ratio: 11.19, 95% Confidence Interval: 3.72-33.62, log-rank p < 0.0001) after surgery. We further showed that the 5hmC-based prognostic scores demonstrated a superior capability for predicting patients’ overall survival compared to existing clinical prognostic factors, such as tumor stage and CA19-9 levels. Exploring these prognostic genes using the Human Pathology Atlas for PDAC patients showed that several genes were significantly associated with the five-year survival for PDAC patients from The Cancer Genome Atlas (log-rank p < 0.001), including SEPHS1 (encoding selenophosphate synthetase 1), PFDN5 (encoding prefoldin subunit 5), and MTERF4 (Mitochondrial transcription termination factor 4). Though limited by the relatively short follow-up time in this study, our exploration suggested that the 5hmC profiles of a 12-gene prognostic panel in cfDNA could help differentiate patients with PDAC by their overall survival after surgery. More comprehensive follow-up investigations will ultimately establish the prognostic utility of this noninvasive approach for precision care of PDAC in the clinic. Citation Format: Zhou Zhang, Lei You, Xingyu Lu, Yanqun Song, Chang Zeng, Rudy Chiu, Wenhui Lou, Chuan He, Yupei Zhao. Genome-wide 5-hydroxymethylcytosine mapping in circulating cell-free DNA reveals prognostic implications in pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr B67.

Genomic signatures and candidate genes of lint yield and fibre quality improvement in Upland cotton in Xinjiang.

SummaryXinjiang has been the largest and highest yield cotton production region not only in China, but also in the world. Improvements in Upland cotton cultivars in Xinjiang have occurred via pedigree selection and/or crossing of elite alleles from the former Soviet Union and other cotton producing regions of China. But it is unclear how genomic constitutions from foundation parents have been selected and inherited. Here, we deep‐sequenced seven historic foundation parents, comprising four cultivars introduced from the former Soviet Union (108Ф, C1470, 611Б and KK1543) and three from United States and Africa (DPL15, STV2B and UGDM), and re‐sequenced sixty‐nine Xinjiang modern cultivars. Phylogenetic analysis of more than 2 million high‐quality single nucleotide polymorphisms allowed their classification two groups, suggesting that Xinjiang Upland cotton cultivars were not only spawned from 108Ф, C1470, 611Б and KK1543, but also had a close kinship with DPL15, STV2B and UGDM. Notably, identity‐by‐descent (IBD) tracking demonstrated that the former Soviet Union cultivars have made a huge contribution to modern cultivar improvement in Xinjiang. A total of 156 selective sweeps were identified. Among them, apoptosis‐antagonizing transcription factor gene (GhAATF1) and mitochondrial transcription termination factor family protein gene (GhmTERF1) were highly involved in the determination of lint percentage. Additionally, the auxin response factor gene (GhARF3) located in inherited IBD segments from 108Ф and 611Б was highly correlated with fibre quality. These results provide an insight into the genomics of artificial selection for improving cotton production and facilitate next‐generation precision breeding of cotton and other crops.

Value of human mitochondrial transcription termination factor 3 and forkhead box protein 3 in predicting the prognosis of non-small cell lung cancer

Objective To explore the prognostic value of human mitochondrial transcription termination factor 3 (hMTERF3) and forkhead box protein 3 (Foxp3) in non-small cell lung cancer (NSCLC). Methods The clinical data of 88 patients with NSCLC who were admitted to the Third Medical Center of PLA General Hospital from March 2017 to March 2018 were retrospectively analyzed. All patients were diagnosed by pathological puncture. The patients were followed-up by telephone for 12 months, and according to the prognosis, the patients were divided into good prognosis group and poor prognosis group. The pathological tissues were taken from all patients, and the expressions of hMTERF3 and Foxp3 proteins were detected by immunohistochemistry. The expressions of hMTERF3 and Foxp3 in the good prognosis group and the poor prognosis group were compared. Logistic regression model was used to analyze the risk factors of poor prognosis in patients with NSCLC. Results Of 88 patients, 61 patients (69.3%) had good prognosis and 27 patients (30.7%) had poor prognosis. The positive expression rate of hMTERF3 in the good prognosis group was 57.4% (35/61), which was significantly lower than that in the poor prognosis group (81.5%, 22/27) (χ 2= 4.766, P= 0.029). The positive expression rate of Foxp3 in the good prognosis group was 55.7% (34/61), which was significantly lower than that in the poor prognosis group (85.2%, 23/27) (χ 2= 7.113, P= 0.008). The proportions of patients with medium and high differentiation or stage Ⅰ- Ⅱ in the good prognosis group were 82.0% (50/61) and 68.8% (42/61), respectively, which were significantly higher than those in the poor prognosis group [48.15% (13/27) and 25.93% (7/27)] (both P < 0.05). Logistic regression analysis showed that the poor differentiation, stage Ⅲ-Ⅳ, hMTERF3-positive and Foxp3-positive were the risk factors for poor prognosis in NSCLC patients (all P < 0.05). Conclusions The positive expression rates of hMTERF3 and Foxp3 in patients with good prognosis are lower. The hMTERF3-positive and Foxp3-positive are risk factors for poor prognosis in NSCLC patients. Key words: Carcinoma, non-small-cell lung; Mitochondrial proteins; Forkhead transcription factors; Human mitochondrial transcription termination factor 3; Forkhead box protein 3; Prognosis

Precise annotation of human, chimpanzee, rhesus macaque and mouse mitochondrial genomes leads to insight into mitochondrial transcription in mammals

ABSTRACTIn the present study, we applied our ‘precise annotation’ to the mitochondrial (mt) genomes of human, chimpanzee, rhesus macaque and mouse using 5′ and 3′ end small RNAs. Our new annotations updated previous annotations. In particular, our new annotations led to two important novel findings: (1) the identification of five Conserved Sequence Blocks (CSB1, CSB2, CSB3, LSP and HSP) in the control regions; and (2) the annotation of Transcription Initiation and novel Transcription Termination Sites. Based on these annotations, we proposed a novel model of mt transcription which can account for the mt transcription and its regulation in mammals. According to our model, Transcription Termination Sites function as switches to regulate the production of short, long primary transcripts and uninterrupted transcription, rather than simply terminate the mt transcription. Moreover, the expression levels of mitochondrial transcription termination factors control the proportions of rRNAs, mRNAs and lncRNAs in total mt RNA. Our findings point to the existence of many other, as yet unidentified, Transcription Termination Sites in mammals.

Functional analysis of mTERF5 and mTERF9 contribution to salt tolerance, plastid gene expression and retrograde signalling in Arabidopsis thaliana.

We previously showed that Arabidopsis mda1 and mterf9 mutants, defective in the chloroplast-targeted mitochondrial transcription termination factors mTERF5 and mTERF9, respectively, display altered responses to abiotic stresses and abscisic acid (ABA), as well as perturbed development, likely through abnormal chloroplast biogenesis. To advance the functional analysis of mTERF5 and mTERF9, we obtained and characterized overexpression (OE) lines. Additionally, we studied genetic interactions between sca3-2, affected in the plastid-RNA polymerase RpoTp, and the mda1-1 and mterf9 mutations. We also investigated the role of mTERF5 and mTERF9 in plastid translation and plastid-to-nucleus signalling. We found that mTERF9 OE reduces salt and ABA tolerance, while mTERF5 or mTERF9 OE alter expression of nuclear and plastid genes. We determined that mda1-1 and mterf9 mutations genetically interact with sca3-2. Further, plastid 16S rRNA levels were reduced in mda1-1 and mterf9 mutants, and mterf9 was more sensitive to chemical inhibitors of chloroplast translation. Expression of the photosynthesis gene LHCB1, a retrograde signalling marker, was differentially affected in mda1-1 and/or mterf9 compared to wild-type Col-0, after treatments with inhibitors of carotenoid biosynthesis (norflurazon) or chloroplast translation (lincomycin). Moreover, mterf9, but not mda1-1, synergistically interacts with gun1-1, defective in GUN1, a central integrator of plastid retrograde signals. Our results show that mTERF9, and to a lesser extent mTERF5, are negative regulators of salt tolerance and that both genes are functionally related to RpoTp, and that mTERF9 is likely required for plastid ribosomal stability and/or assembly. Furthermore, our findings support a role for mTERF9 in retrograde signalling.

Characterization of mTERF family in allotetraploid peanut and their expression levels in response to dehydration stress

Polyploidization events are prevalent in plants and act as an important evolutionary force for speciation, adaptation and diversification. During this process, the genome undergoes reorganization and large changes. However, the evolutionary characteristics of specific gene families are still not well investigated. Cultivated peanut is an allotetraploid that evolved from a diploid. In this study, we focused on the family of mitochondrial transcription termination factors (mTERF), which is increasing in gene number in higher plants and acts in organellar gene expression. The 65 mTERFs were identified in allotetraploid peanut, but only 31 in diploid peanut, which showed that the genome has not doubled simply during the polyploidization event. Some of the mTERFs may have emerged as a result of reverse complements, deletions, insertions, fusions and so on. mTERFs were divided into three groups according to their predicted localization. Six representative proteins showed their different localization. Most of the AhmTERF mRNAs were detected in root and leaf samples and responded to dehydration stress. Our data provide insights into the evolution of the mTERF gene family in peanut and further support the hypothesis that these genes respond to dehydration stress.

Genome-Wide Identification and Characterization of the Mitochondrial Transcription Termination Factors (mTERFs) in Capsicum annuum L.

Mitochondrial transcription termination factors (mTERFs) regulate the expression of mitochondrial genes and are closely related to the function of the mitochondrion and chloroplast. In this study, the mTERF gene family in capsicum (Capsicum annuum L.) was identified and characterized through genomic and bioinformatic analyses. Capsicum was found to possess at least 35 mTERF genes (CamTERFs), which were divided into eight major groups following phylogenetic analysis. Analysis of CamTERF promoters revealed the presence of many cis-elements related to the regulation of cellular respiration and photosynthesis. In addition, CamTERF promoters contained cis-elements related to phytohormone regulation and stress responses. Differentially expressed genes in different tissues and developmental phases were identified using RNA-seq data, which revealed that CamTERFs exhibit various expression and co-expression patterns. Gene ontology (GO) annotations associated CamTERFs primarily with mitochondrion and chloroplast function and composition. These results contribute towards understanding the role of mTERFs in capsicum growth, development, and stress responses. Moreover, our data assist in the identification of CamTERFs with important functions, which opens avenues for future studies.

Crown morphology in Norway spruce (Picea abies [Karst.] L.) as adaptation to mountainous environments is associated with single nucleotide polymorphisms (SNPs) in genes regulating seasonal growth rhythm

Trees growing at high altitude or latitude have to be adapted, among others, to the lower temperatures, a shorter vegetation period, heavier snow load, and frost desiccation. Association between molecular genetic markers and climatic variables may provide evidence for the genetic control of climatic adaptation. With increasing genomic resources, several genes with importance to climatic adaptation are identified over a wide range of tree species. Commonly, circadian clock genes are linked to the adaptation to lower temperatures and especially to a shortened vegetation period, as they are regulating metabolic and phenological processes in the day–night shift and seasonal change. Potentially adaptive “candidate” genes associated with latitudinal and elevational gradients were identified in several Picea spp. Before molecular markers became available to study climatic adaptation and phenotypic traits measured in natural populations, and/or common garden studies were used to search for their association with climate variables. In Norway spruce, the crown architecture is the most noticeable trait associated with altitude and the related environment. The mountainous narrow-crowned morphotype is characterized by superior resistance to snow breakage in regions with heavy snowfall. In total, the crown shape was assessed in 765 individual trees from mountainous regions in the Thuringian Forest, the Ore Mountains (Saxony), and Harz Mountains (Lower-Saxony/Saxony-Anhalt), and they were genotyped at 44 single nucleotide polymorphisms (SNPs) in 24 adaptive trait-related candidate genes. Six SNPs in three genes, APETALA 2-like 3 (AP2L3), GIGANTEA (GI), and mitochondrial transcription termination factor (mTERF) were associated with variation in crown shape. GI has previously been identified in angiosperms and gymnosperms to be associated with temperature and growth cessation. Our results showed that crown morphology in Norway spruce is associated with genetic markers which are putatively involved in the complex process of genetic adaptation to climatic conditions at high altitudes.

MTERF8, a Member of the Mitochondrial Transcription Termination Factor Family, Is Involved in the Transcription Termination of Chloroplast Gene psbJ.

Members of the mitochondrial transcription terminator factor (mTERF) family, originally identified in vertebrate mitochondria, are involved in the termination of organellular transcription. In plants, mTERF proteins are mainly localized in chloroplasts and mitochondria. In Arabidopsis (Arabidopsis thaliana), mTERF8/pTAC15 was identified in the plastid-encoded RNA polymerase (PEP) complex, the major RNA polymerase of chloroplasts. In this work, we demonstrate that mTERF8 is associated with the PEP complex. An mTERF8 knockout line displayed a wild-type-like phenotype under standard growth conditions, but showed impaired efficiency of photosystem II electron flow. Transcription of most chloroplast genes was not substantially affected in the mterf8 mutant; however, the level of the psbJ transcript from the psbEFLJ polycistron was increased. RNA blot analysis showed that a larger transcript accumulates in mterf8 than in the wild type. Thus, abnormal transcription and/or RNA processing occur for the psbEFLJ polycistron. Circular reverse transcription PCR and sequence analysis showed that the psbJ transcript terminates 95 nucleotides downstream of the translation stop codon in the wild type, whereas its termination is aberrant in mterf8 Both electrophoresis mobility shift assays and chloroplast chromatin immunoprecipitation analysis showed that mTERF8 specifically binds to the 3' terminal region of psbJ Transcription analysis using the in vitro T7 RNA polymerase system showed that mTERF8 terminates psbJ transcription. Together, these results suggest that mTERF8 is specifically involved in the transcription termination of the chloroplast gene psbJ.

The Complete Mitogenome of Pyrrhocoris tibialis (Hemiptera: Pyrrhocoridae) and Phylogenetic Implications.

We determined the complete mitogenome of Pyrrhocoris tibialis (Hemiptera: Heteroptera: Pyrrhocoridae) to better understand the diversity and phylogeny within Pentatomomorpha, which is the second largest infra-order of Heteroptera. Gene content, gene arrangement, nucleotide composition, codon usage, ribosomal RNA (rRNA) structures, and sequences of the mitochondrial transcription termination factor were well conserved in Pyrrhocoroidea. Different protein-coding genes have been subject to different evolutionary rates correlated with the G + C content. The size of control regions (CRs) was highly variable among mitogenomes of three sequenced Pyrrhocoroidea species, with the P. tibialis CR being the largest. All the transfer RNA genes found in Pyrrhocoroidea had the typical clover leaf secondary structure, except for trnS1 (AGN), which lacked the dihydrouridine arm and possessed an unusual anticodon stem (9 bp vs. the normal 5 bp). A total of three different phylogenetic relationships among the five super-families of Pentatomomorpha were obtained using three analytical methods (MrBayes and RAxML under site-homogeneous models and PhyloBayes under a site-heterogeneous CAT + GTR model) and two mitogenomic datasets (nucleotides and amino acids). The tree topology test using seven methods statistically supported a phylogeny of (Aradoidea + (Pentatomoidea + (Lygaeoidea + (Pyrrhocoroidea + Coreoidea)))) as the best topology, as recognized by both RAxML and MrBayes based on the two datasets.

A Mitochondrial Transcription Termination Factor, ZmSmk3, Is Required for nad1 Intron4 and nad4 Intron1 Splicing and Kernel Development in Maize.

The expression systems of the mitochondrial genes are derived from their bacterial ancestors, but have evolved many new features in their eukaryotic hosts. Mitochondrial RNA splicing is a complex process regulated by families of nucleus-encoded RNA-binding proteins, few of which have been characterized in maize (Zea mays L.). Here, we identified the Zea mays small kernel 3 (Zmsmk3) candidate gene, which encodes a mitochondrial transcription termination factor (mTERF) containing two mTERF motifs, which is conserved in monocotyledon; and the target introns were also quite conserved during evolution between monocotyledons and dicotyledons. The mutations of Zmsmk3 led to arrested embryo and endosperm development, resulting in small kernels. A transcriptome of 12 days after pollination endosperm analysis revealed that the starch biosynthetic pathway and the zein gene family were down-regulated in the Zmsmk3 mutant kernels. ZmSMK3 is localized in mitochondria. The reduced expression of ZmSmk3 in the mutant resulted in the splicing deficiency of mitochondrial nad4 intron1 and nad1 intron4, causing a reduction in complex I assembly and activity, impairing mitochondria structure and activating the alternative respiratory pathway. So, the results suggest that ZmSMK3 is required for the splicing of nad4 intron 1 and nad1 intron 4, complex I assembly and kernel development in maize.

Prognostic roles of mitochondrial transcription termination factors in non-small cell lung cancer.

Mitochondrial transcription termination factors (MTERFs) regulate mitochondrial gene transcription and metabolism in numerous types of cells. Previous studies have indicated that MTERFs serve pivotal roles in the pathogenesis of various cancer types. However, the expression and prognostic roles of MTERFs in patients with non-small cell lung cancer (NSCLC) remain elusive. The present study investigated the gene alteration frequency and expression level using Gene Expression Omnibus datasets and reverse transcription-quantitative polymerase chain reaction, and evaluated the prognostic roles of MTERFs in patients with NSCLC using the Kaplan-Meier plotter database. In human lung cancer tissues, it was observed that the mRNA levels of MTERF1, 2, 3 and 4 were positively associated with the copy number of these genes. The mRNA expression levels of MTERF1 and 3 were significantly increased in NSCLC tissues compared with adjacent non-tumor tissues; however, the mRNA expression of MTERF2 was significantly decreased in NSCLC tissues. High mRNA expression levels of MTERF1, 2, 3 and 4 were strongly associated with an improved overall survival rate (OS) in patients with lung adenocarcinoma. Additionally, high mRNA expression levels of MTERF1, 2, 3 and 4 were also strongly associated with an improved OS of patients with NSCLC in the earlier stages of disease (stage I) or patients with negative surgical margins. These results indicate the critical prognostic values of MTERF expression levels in NSCLC. The findings of the present study may be beneficial for understanding the molecular biology mechanism of NSCLC and for generating effective therapeutic approaches for patients with NSCLC.

Transcriptome wide characterization of water deficit responsive grape mTERF transcription

Plant mitochondrial transcription termination factor (mTERF) is a large and important family with valuable roles in organizing of organelle gene expression under the various stresses. In this study, genome wide analysis of mTERF regulatory genes was achieved and twenty-five potential mTERF genes response water deficit in grape (Vitis vinifera L.) were determined. Most of them were targeted to organelles genome especially mitochondria. It was found that Grape mTERFs were clustered into six main groups based on phylogenetic analysis. As a result of comprehensive expression analysis of these genes, using RNA-seq data in this study revealed that these genes have various expression profiles. With this study, various important roles of mTERF genes of grape under the water deficit stress were reported at first in grape. All results were found will be useful for elucidating the roles of mTERF genes in the growth, development and stress response of grape and fundamental for functional genomic studies.

Analysis of the coding sequences of clownfish reveals molecular convergence in the evolution of lifespan

BackgroundStandard evolutionary theories of aging postulate that reduced extrinsic mortality leads to evolution of longevity. Clownfishes of the genus Amphiprion live in a symbiotic relationship with sea anemones that provide protection from predators. We performed a survey and identified at least two species with a lifespan of over 20 years. Given their small size and ease of captive reproduction, clownfish lend themselves as experimental models of exceptional longevity. To identify genetic correlates of exceptional longevity, we sequenced the transcriptomes of Amphiprion percula and A. clarkii and performed a scan for positively-selected genes (PSGs).ResultsThe PSGs that we identified in the last common clownfish ancestor were compared with PSGs detected in long-lived mole rats and short-lived killifishes revealing convergent evolution in processes such as mitochondrial biogenesis. Among individual genes, the Mitochondrial Transcription Termination Factor 1 (MTERF1), was positively-selected in all three clades, whereas the Glutathione S-Transferase Kappa 1 (GSTK1) was under positive selection in two independent clades. For the latter, homology modelling strongly suggested that positive selection targeted enzymatically important residues.ConclusionsThese results indicate that specific pathways were recruited in independent lineages evolving an exceptionally extended or shortened lifespan and point to mito-nuclear balance as a key factor.

Transcriptome Profile of the Variegated Ficus microcarpa c.v. Milky Stripe Fig Leaf.

Photosynthetic properties and transcriptomic profiles of green and white sectors of Ficus microcarpa (c.v. milky stripe fig) leaves were examined in naturally variegated plants. An anatomic analysis indicated that chloroplasts of the white sectors contained a higher abundance of starch granules and lacked stacked thylakoids. Moreover, no photosynthetic rate was detected in the white sectors. Transcriptome profile and differential expressed gene (DEG) analysis showed that genes encoding PSII core proteins were down-regulated in the white sectors. In genes related to chlorophyll metabolism, no DEGs were identified in the biosynthesis pathway of chlorophyll. However, genes encoding the first step of chlorophyll breakdown were up-regulated. The repression of genes involved in N-assimilation suggests that the white sectors were deprived of N. The mutation in the transcription factor mitochondrial transcription termination factor (mTERF) suggests that it induces colorlessness in leaves of the milky stripe fig.