Internal Repeats Research Articles

Development of a bacterial artificial chromosome (BAC) recombineering procedure using galK-untranslated region (UTR) for the mutation of diploid genes

Bacterial artificial chromosome (BAC) recombineering using galK selection allows DNA cloned in Escherichia coli to be modified without introducing an unwanted selectable marker at the modification site. Genomes of some herpesviruses have a pair of inverted repeat sequences that makes it very difficult to introduce mutations into diploid (duplicate) genes using the galK selection method. To mutate diploid genes, we developed a galK-UTR BAC recombineering procedure that blocks one copy of the target diploid gene by insertion of a galK untranslated region (UTR), which enables the simple mutation of the other copy. The blocked copy can then be replaced with an UTR-specific primer pair. The IR2 gene of equine herpesvirus 1 (EHV-1) maps within both the internal (IR) and terminal repeat (TR) of the genomic short region and is expressed at low levels because its promoter is TATA-less. Both IR2 promoters in EHV-1 BAC were replaced with a mutant IR2 promoter containing three Sp1-binding motifs and a consensus TATA box by galK-UTR BAC recombineering. The expression level of the IR2 protein controlled by the modified promoter increased approximately 4-fold as compared to that of wild-type EHV-1. The galK-UTR method will provide a useful tool in studies of herpesviruses.

Assessing genetic diversity in the web blight pathogen Thanatephorus cucumeris (anamorph = Rhizoctonia solani) subgroups AG-1-IE and AG-1-IF with molecular markers

Web blight, an important foliar disease of dry beans in the Americas, is a challenge to manage. We studied genetic variation of 92 isolates of Rhizoctonia solani subgroups AG-1-IE and AG-1-IF using DNA fingerprinting methods and mycelial compatibility grouping. The isolates were collected over 13 years from bean fields in the Dominican Republic, Honduras and Puerto Rico. Cluster and AMOVA analysis of combined data from two universal rice primers and two internal sequence repeats revealed significant genetic variation among and within populations of both subgroups. Variation was influenced by geographic origin and sampling year for AG-1-IE isolates and geographic origin for AG-1-IF isolates. Mycelial compatibility of paired isolates was mostly scored as incompatible in both subgroups and supported many unique phenotypes. Only two isolates of AG-1-IE displayed mycelial compatibility and DNA fingerprints, suggesting clonal origin. Genetic variation in these AG-1-IE and AG-1-IF isolate populations may explain the lack of durable resistance to web blight reported in dry beans.

The Internal Region Leucine-rich Repeat 6 of Decorin Interacts with Low Density Lipoprotein Receptor-related Protein-1, Modulates Transforming Growth Factor (TGF)-β-dependent Signaling, and Inhibits TGF-β-dependent Fibrotic Response in Skeletal Muscles

Decorin is a small proteoglycan, composed of 12 leucine-rich repeats (LRRs) that modulates the activity of transforming growth factor type β (TGF-β) and other growth factors, and thereby influences proliferation and differentiation in a wide array of physiological and pathological processes, such as fibrosis, in several tissues and organs. Previously we described two novel modulators of the TGF-β-dependent signaling pathway: LDL receptor-related protein (LRP-1) and decorin. Here we have determined the regions in decorin that are responsible for interaction with LRP-1 and are involved in TGF-β-dependent binding and signaling. Specifically, we used decorin deletion mutants, as well as peptides derived from internal LRR regions, to determine the LRRs responsible for these decorin functions. Our results indicate that LRR6 and LRR5 participate in the interaction with LRP-1 and TGF-β as well as in its dependent signaling. Furthermore, the internal region (LRR6i), composed of 11 amino acids, is responsible for decorin binding to LRP-1 and subsequent TGF-β-dependent signaling. Furthermore, using an in vivo approach, we also demonstrate that the LRR6 region of decorin can inhibit TGF-β mediated action in response to skeletal muscle injury.

Determinants of Small Ubiquitin-like Modifier 1 (SUMO1) Protein Specificity, E3 Ligase, and SUMO-RanGAP1 Binding Activities of Nucleoporin RanBP2

The RanBP2 nucleoporin contains an internal repeat domain (IR1-M-IR2) that catalyzes E3 ligase activity and forms a stable complex with SUMO-modified RanGAP1 and UBC9 at the nuclear pore complex. RanBP2 exhibits specificity for SUMO1 as RanGAP1-SUMO1/UBC9 forms a more stable complex with RanBP2 compared with RanGAP1-SUMO2 that results in greater protection of RanGAP-SUMO1 from proteases. The IR1-M-IR2 SUMO E3 ligase activity also shows a similar preference for SUMO1. We utilized deletions and domain swap constructs in protease protection assays and automodification assays to define RanBP2 domains responsible for RanGAP1-SUMO1 protection and SUMO1-specific E3 ligase activity. Our data suggest that elements in both IR1 and IR2 exhibit specificity for SUMO1. IR1 protects RanGAP1-SUMO1/UBC9 and functions as the primary E3 ligase of RanBP2, whereas IR2 retains the ability to interact with SUMO1 to promote SUMO1-specific E3 ligase activity. To determine the structural basis for SUMO1 specificity, a hybrid IR1 construct and IR1 were used to determine three new structures for complexes containing UBC9 with RanGAP1-SUMO1/2. These structures show more extensive contacts among SUMO, UBC9, and RanBP2 in complexes containing SUMO1 compared with SUMO2 and suggest that differences in SUMO specificity may be achieved through these subtle conformational differences.

Using hierarchical clustering of secreted protein families to classify and rank candidate effectors of rust fungi.

Rust fungi are obligate biotrophic pathogens that cause considerable damage on crop plants. Puccinia graminis f. sp. tritici, the causal agent of wheat stem rust, and Melampsora larici-populina, the poplar leaf rust pathogen, have strong deleterious impacts on wheat and poplar wood production, respectively. Filamentous pathogens such as rust fungi secrete molecules called disease effectors that act as modulators of host cell physiology and can suppress or trigger host immunity. Current knowledge on effectors from other filamentous plant pathogens can be exploited for the characterisation of effectors in the genome of recently sequenced rust fungi. We designed a comprehensive in silico analysis pipeline to identify the putative effector repertoire from the genome of two plant pathogenic rust fungi. The pipeline is based on the observation that known effector proteins from filamentous pathogens have at least one of the following properties: (i) contain a secretion signal, (ii) are encoded by in planta induced genes, (iii) have similarity to haustorial proteins, (iv) are small and cysteine rich, (v) contain a known effector motif or a nuclear localization signal, (vi) are encoded by genes with long intergenic regions, (vii) contain internal repeats, and (viii) do not contain PFAM domains, except those associated with pathogenicity. We used Markov clustering and hierarchical clustering to classify protein families of rust pathogens and rank them according to their likelihood of being effectors. Using this approach, we identified eight families of candidate effectors that we consider of high value for functional characterization. This study revealed a diverse set of candidate effectors, including families of haustorial expressed secreted proteins and small cysteine-rich proteins. This comprehensive classification of candidate effectors from these devastating rust pathogens is an initial step towards probing plant germplasm for novel resistance components.

A Role for the Internal Repeat of the Kaposi's Sarcoma-Associated Herpesvirus Latent Nuclear Antigen in the Persistence of an Episomal Viral Genome

The latent nuclear antigen (LANA) of Kaposi's sarcoma-associated herpesvirus (KSHV) is required for the replication and partitioning of latent viral genomes. It contains an extended internal repeat (IR) region whose function is only incompletely understood. We constructed KSHV genomes lacking either LANA (KSHV-ΔLANA) or the IR region of LANA (KSHV-LANAΔ329-931). Although still capable of replicating a plasmid containing a latent origin of replication, LANAΔ329-931 does not support the establishment of stable cell lines containing a KSHV genome. These findings suggest a role for the LANA IR in KSHV episomal maintenance without its being required for replication.

Identification and synthesis of novel biomaterials based on spider structural silk fibers

The diversity in function and mechanical behavior of spider silks, and the ability to produce these silks recombinantly, have tremendous potential in creating a new class of biomimetic materials. Here we investigate the structural and mechanical properties of pyriform silks from the golden orb-weaver, Nephila clavipes. Nanoscale indentation measurements using atomic force microscopy on natural pyriform silk suggests that this biomaterial has high toughness that may be suitable for dissipating high amounts of mechanical energy. We also observed the occurrence of highly organized nanocrystals within the pyriform silk fibers that may contribute to the remarkable energy dissipation capability of these silks. It has been demonstrated that poly-(Gly–Ala) and poly-Ala stretches within the internal block repeat modules of dragline silk fibroins form nanocrystals, and these nanocrystalline structures may be responsible for the high extensibility of the dragline silks. In contrast, amino acid sequence analysis shows that PySp2 does not contain the same motifs. In the absence of poly-(Gly–Ala) and poly-Ala repeats, we hypothesized that PySp2 contains new protein motifs sufficient to polymerize into functional structures. To investigate the functional contributions of these novel motifs during pyriform fiber formation, we expressed different recombinant PySp2 fibroins with various segments spanning its block repeat units. We demonstrate that PySp2 recombinant proteins with the Pro-rich sub-block domain (PXP motifs, where X= sub-set of the amino acids A, L, or R) and/or the Ser + Gln + Ala-rich sub-block domain (QQSSVAQS motifs) are sufficient for artificial fiber formation. Moreover, we show that recombinant PySp2 proteins that contain a single block repeat unit can self-assemble into foam-like nanostructures. Collectively, our findings support the use of PySp2 recombinant proteins for a wide range of biomimetic materials with morphologies ranging from fibers to porous structures.

Identification of latent periodicity in domains of alkaline proteases

Internal repeats in protein sequences have wide-ranging implications for the structure and function of proteins. A keen analysis of the repeats in protein sequences may help us to better understand the structural organization of proteins and their evolutionary relations. In this paper, a mathematical method for searching for latent periodicity in protein sequences is developed. Using this method, we identified simple sequence repeats in the alkaline proteases and found that the sequences could show the same periodicity as their tertiary structures. This result may help us to reduce difficulties in the study of the relationship between sequences and their structures.

Isolation and characterization of a new repetitive DNA family recently amplified in the Mesoamerican gene pool of the common bean (Phaseolus vulgaris L., Fabaceae)

The common bean (Phaseolus vulgaris) is one of the most important crop plants. About 50% of its genome is composed of repetitive sequences, but only a little fraction was isolated and characterized so far. In this paper, a new repetitive DNA family from the species, named PvMeso, was isolated and characterized in both gene pools of P. vulgaris (Andean and Mesoamerican) and related species. Two fragments, 1.7 and 2.3 kb long, were cloned from BAC 255F18, which has previously shown a repetitive pattern. The subclone PvMeso-31 showed a terminal block in chromosome 7. This subclone contains a 1,705 bp long, AT-rich repeat with small internal repeats and shares a 1.2 kb region with PvMeso-47, derived from the 2.3 kb fragment. The presence of this repetitive block was restricted to Mesoamerican accessions of the common bean. In P. acutifolius, P. leptostachyus and Andean P. vulgaris, only a faint, 2.3 kb fragment was visualized in Southern experiments. Moreover, in Mesoamerican accessions, two other fragments (1.7 kb and 3.4 kb) were strongly labelled as well. Taken together, our results indicate that PvMeso is a recently emerged, repeat family initially duplicated in chromosome 11, on ancestral Mesoamerican accession, and later amplified in chromosome 7, after the split of the two major gene pools of the common bean.

DNA sequence requirements for hobo transposable element transposition in Drosophila melanogaster

We have conducted a structure and functional analysis of the hobo transposable element of Drosophila melanogaster. A minimum of 141 bp of the left (L) end and 65 bp of the right (R) end of the hobo were shown to contain sequences sufficient for transposition. Both ends of hobo contain multiple copies of the motifs GGGTG and GTGGC and we show that the frequency of hobo transposition increases as a function of the copy number of these motifs. The R end of hobo contains a unique 12 bp internal inverted repeat that is identical to the hobo terminal inverted repeats. We show that this internal inverted repeat suppresses transposition activity in a hobo element containing an intact L end and only 475 bp of the R end. In addition to establishing cis-sequences requirements for transposition, we analyzed trans-sequence effects of the hobo transposase. We show a hobo transposase lacking the first 49 amino acids catalyzed hobo transposition at a higher frequency than the full-length transposase suggesting that, similar to the related Ac transposase, residues at the amino end of the transposase reduce transposition. Finally, we compared target site sequences of hobo with those of the related Hermes element and found both transposons have strong preferences for the same insertion sites.

Site‐specific accretion of an integrative conjugative element together with a related genomic island leads to cis mobilization and gene capture

Genomic islands, flanked by attachment sites, devoid of conjugation and recombination modules and related to the integrative and conjugative element (ICE) ICESt3, were previously found in Streptococcus thermophilus. Here, we show that ICESt3 transfers to a recipient harbouring a similar engineered genomic island, CIMEL₃catR₃, and integrates by site-specific recombination into its attachment sites, leading to their accretion. The resulting composite island can excise, showing that ICESt3 mobilizes CIMEL₃catR₃, in cis. ICESt3, CIMEL₃catR₃, and the whole composite element can transfer from the strain harbouring the composite structure. The ICESt3 transfer to a recipient bearing CIMEL₃catR₃, can also lead to retromobilization, i.e. its capture by the donor. This is the first demonstration of specific conjugative mobilization of a genomic island in cis and the first report of ICE-mediated retromobilization. CIMEL₃catR₃, would be the prototype of a novel class of non-autonomous mobile elements (CIMEs: CIs mobilizable elements), which hijack the recombination and conjugation machinery of related ICEs to excise, transfer and integrate. Few genome analyses have shown that CIMEs could be widespread and have revealed internal repeats that could result from accretions in numerous genomic islands, suggesting that accretion and cis mobilization have a key role in evolution of genomic islands.

KL1 Internal Repeat Mediates Klotho Tumor Suppressor Activities and Inhibits bFGF and IGF-I Signaling in Pancreatic Cancer

Klotho is a transmembrane protein which can be shed, act as a circulating hormone and modulate the insulin-like growth factor (IGF)-I and the fibroblast growth factor (FGF) pathways. We have recently identified klotho as a tumor suppressor in breast cancer. Klotho is expressed in the normal pancreas and both the IGF-I and FGF pathways are involved in pancreatic cancer development. We, therefore, undertook to study the expression and activity of klotho in pancreatic cancer. Klotho expression was studied using immunohistochemistry and quantitative RT-PCR. Effects of klotho on cell growth were assessed in the pancreatic cancer cells Panc1, MiaPaCa2, and Colo357, using colony and MTT assays and xenograft models. Signaling pathway activity was measured by Western blotting. Klotho expression is downregulated in pancreatic adenocarcinoma. Overexpression of klotho, or treatment with soluble klotho, reduced growth of pancreatic cancer cells in vitro and in vivo, and inhibited activation of the IGF-I and the bFGF pathways. KL1 is a klotho subdomain formed by cleavage or alternative splicing. Compared with the full-length protein, KL1 showed similar growth inhibitory activity but did not promote FGF23 signaling. Thus, its administration to mice showed favorable safety profile. These studies indicate klotho as a potential tumor suppressor in pancreatic cancer, and suggest, for the first time, that klotho tumor suppressive activities are mediated through its KL1 domain. These results suggest the use of klotho or KL1 as potential strategy for the development of novel therapeutic interventions for pancreatic cancer.

Highlights of This Issue

To explore the value of HER2 as a target in ovarian cancer, Faratian and colleagues evaluated the combination of the HER2-directed antibodies trastuzumab and pertuzumab in xenograft models. They found that the antibody combination was effective against high HER2-expressing tumors. Size, apoptosis, morphology, and estrogenregulated gene expression were modulated by the antibodies in a spatial and temporal manner. Further, trastuzumab increased ERα expression and enhanced sensitivity to letrozole. These results suggest that trastuzumab in combination with pertuzumab could be an effective treatment for high HER2-expressing ovarian cancers, and could also enhance sensitivity to endocrine therapy in ERα-positive ovarian cancer.Klotho is a transmembrane protein that can be shed and act as a circulating hormone. Here, Abramovitz and colleagues explored the expression and function of klotho in pancreatic cancer. They found that klotho expression was reduced in human pancreatic adenocarcinoma. Treatment with klotho or with KL1 internal repeat effectively slowed the growth of pancreatic cancer cells in vitro and in vivo and inhibited activation of the IGF-1 and FGF pathways. These findings indicate that klotho acts as a tumor suppressor and suggest that klotho may be used therapeutically or as a diagnostic marker in pancreatic cancer.In this issue, Kyte and colleagues report a trial evaluating combined therapy with temozolomide and the telomerase peptide vaccine GV1001 in advanced melanoma patients. They found that 18 of 23 subjects developed a telomerase-specific immune response, without notable toxicity. Patients developing longterm immunologic memory survived longer than those who rapidly lost immune response. Five patients developed partial tumor regression and overall survival (intention-totreat population) was extended compared with matched controls from a benchmark meta-analysis. These findings warrant further studies of GV1001/temozolomide treatment and support the concept of combining cancer vaccination with chemotherapy.Variable individual response to opioid therapy for cancer pain is an important problem in the clinical management of patients. In this issue, Galvan and colleagues carried out a genome-wide association study in 1,008 cancer patients undergoing opioid therapy. They identified eight genetic polymorphisms significantly associated with poor response to opioid therapy. Genes related to nerve impulse transmission rather than genes implicated in opioid pharmacology were tagged. These findings may represent a starting point to define therapeutic target(s) for countering poor pain relief, leading to improved quality of life for cancer patients.

Automated, Model‐Based Analysis of Uj‐Data for Electrolyte‐Supported SOFC Short‐Stacks

AbstractA simplified model is presented to analyse current–voltage characteristics of electrolyte supported solid oxide fuel cell stacks that run on reformed hydrocarbon fuels such as natural gas. The model takes into account the fuel reforming process, fuel leakages and electrochemical conversions all in an idealised manner, i.e. it assumes thermodynamic equilibrium. However, the model explicitly accounts for parameter variations that are often unavoidable under realistic testing conditions. These variations include changes in the fuel composition, changes in the fuel mass fluxes and changes in the operation temperature. In addition, internal repeat unit resistances as extracted from current–voltage data are compared with the ohmic and polarisation losses obtained from independent electrical impedance measurements data. Since the data analysis is done in a highly automated fashion, large sets of current–voltage data can be compared and ‘normal' data sets can be discriminated from ‘abnormal' ones. The model has the potential to accelerate testing by eliminating variations that lead to corruption and unwanted scattering of current–voltage data.

Investigation of the population structure of Legionella pneumophila by analysis of tandem repeat copy number and internal sequence variation

The population structure of the species Legionella pneumophila was investigated by multilocus variable number of tandem repeats (VNTR) analysis (MLVA) and sequencing of three VNTRs (Lpms01, Lpms04 and Lpms13) in selected strains. Of 150 isolates of diverse origins, 136 (86 %) were distributed into eight large MLVA clonal complexes (VACCs) and the rest were either unique or formed small clusters of up to two MLVA genotypes. In spite of the lower degree of genome-wide linkage disequilibrium of the MLVA loci compared with sequence-based typing, the clustering achieved by the two methods was highly congruent. The detailed analysis of VNTR Lpms04 alleles showed a very complex organization, with five different repeat unit lengths and a high level of internal variation. Within each MLVA-defined VACC, Lpms04 was endowed with a common recognizable pattern with some interesting exceptions. Evidence of recombination events was suggested by analysis of internal repeat variations at the two additional VNTR loci, Lpms01 and Lpms13. Sequence analysis of L. pneumophila VNTR locus Lpms04 alone provides a first-line assay for allocation of a new isolate within the L. pneumophila population structure and for epidemiological studies.

Isolation and characterization of some novel genes of the apolipoprotein A-I family in Japanese eel, Anguilla japonica

Abstract Apolipoproteins such as apolipoprotein (apo) A-I, apoA-IV, and apoE are lipid binding proteins synthesized mainly in the liver and the intestine and play an important role in the transfer of exogenous or endogenous lipids through the circulatory system. To investigate the mechanism of lipid transport in fish, we have isolated some novel genes of the apoA-I family, apoIA-I (apoA-I isoform) 1–11, from Japanese eel by PCR amplification. Some of the isolated genes of apoIA-I corresponded to 28kDa-1 cDNAs which had already been deposited into the database and encoded an apolipoprotein with molecular weight of 28 kDa in the LDL, whereas others seemed to be novel genes. The structural organization of all apoIA-Is consisted of four exons separated by three introns. ApoIA-I10 had a total length of 3232 bp, whereas other genes except for apoIA-I9 ranged from 1280 to 1441 bp. The sequences of apoIA-Is at the exon-intron junctions were mostly consistent with the consensus sequence (GT/AG) at exon-intron boundaries, whereas the sequences of 3′ splice acceptor in intron 1 of apoIA-I1-7 were (AC) but not (AG). The deduced amino acid sequences of all apoIA-Is contained a putative signal peptide and a propeptide of 17 and 5 amino acid residues, respectively. The mature proteins of apoIA-I1-3, 7, and 8 consisted of 237 amino acids, whereas those of apoIA-I4-6 consisted of 239 amino acids. The mature apoIA-I10 sequence showed 65% identity to amino acid sequence of apoIA-I11 which was associated with an apolipoprotein with molecular weight of 23 kDa in the VLDL. All these mature apoIA-I sequences satisfied the common structural features depicted for the exchangeable apolipoproteins such as apoA-I, apoA-IV, and apoE but apoIA-I11 lacked internal repeats 7, 8, and 9 when compared with other members of apoA-I family. Phylogenetic analysis showed that these novel apoIA-Is isolated from Japanese eel were much closer to apoA-I than apoA-IV and apoE, suggesting new members of the apoA-I family.

Abstract 2192: KL1 internal repeat mediates klotho tumor suppressor activities and inhibits bFGF and IGF-1 signaling in pancreatic cancer

Abstract Klotho is a transmembranal protein, which can be cleaved, shed and act as a circulating hormone. Klotho deficient mice present a syndrome of early aging, while overexpression of klotho extends lifespan. Klotho is a potent inhibitor of the insulin growth factor (IGF)-1 and the basic fibroblast growth factor (FGF) pathways. Klotho is also an essential co-factor for the activity of FGF23 and thus serves as a major regulator of phosphate homeostasis. We have recently identified klotho as a tumor suppressor in breast cancer. As klotho is expressed in the normal pancreas and as the IGF-1 and FGF pathways are involved in pancreatic cancer development, we undertook to study the expression and activity of klotho in pancreatic cancer. Immunohistochemistry analysis revealed significantly reduced expression of klotho in pancreatic cancer compared to normal pancreas, and low levels of klotho mRNA were noted in the pancreatic cancer cells Panc1, Colo357 and MiaPaCa2 compared to normal pancreas cells. Further studies revealed that klotho silencing is mediated by epigenetic mechanisms. Overexpression of klotho or treatment with soluble klotho (8pM) reduced clonal growth of pancreatic cancer cell lines, and a synergistic effect was observed in combination with chemotherapeutic drugs. Daily injections of klotho (10μg/kg) inhibited tumor formation of Panc1 cells in athymic mice. Klotho inhibited activation of the IGF-1 pathway in pancreatic cancer cells. As klotho further enhanced growth inhibition by the IGF-1R inhibitor AG1024, modulation of additional signaling pathways by klotho was suspected. Indeed, klotho overexpression inhibited the bFGF pathway in these cells. The extracellular region of klotho is composed of two internal repeats, KL1 and KL2, and each of them can be cleaved and act separately. While both domains share homology to glycosidase, a structural model suggested that only KL1 retains enzymatic activity. While the KL2 domain did not show growth inhibitory activities, KL1 effectively slowed growth of pancreatic cancer cells, both in vitro and in vivo and was found to be a potent inhibitor of the IGF-1 and bFGF pathways. Importantly, KL1 did not promote FGF23 signaling and therefore, in contrary to the full-length protein, its administration to mice did not affect phosphate homeostasis. In conclusion, these studies indicate klotho as a potent tumor suppressor in pancreatic cancer and suggest, for the first time, that klotho growth inhibitory activities are mediated by the KL1 domain, possibly due to its putative enzymatic activities. As the KL1 domain is not involved in regulation of phosphate homeostasis, its administration may serve as a potential safe and effective novel strategy for the treatment of pancreatic cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2192. doi:10.1158/1538-7445.AM2011-2192

Topology models of anion exchanger 1 that incorporate the anti-parallel V-shaped motifs found in the EM structureThis paper is one of a selection of papers published in a Special Issue entitled CSBMCB 53rd Annual Meeting — Membrane Proteins in Health and Disease, and has undergone the Journal’s usual peer review process.

We recently published the three-dimensional structure of the membrane domain of human erythrocyte anion exchanger 1 (AE1) at 7.5 Å resolution, solved by electron crystallography. The structure exhibited distinctive anti-parallel V-shaped motifs, which protrude from the membrane bilayer on both sides. Similar motifs exist in the previously reported structure of a bacterial chloride channel (ClC)-type protein. Here, we propose two topology models of AE1 that reflect the anti-parallel V-shaped structural motifs. One is assumed to have structural similarity with the ClC protein and the other is only assumed to have internal repeats, as is often the case with transporters. Both models are consistent with most topological results reported thus far for AE1, each having advantages and disadvantages.

Artificially inserting a reticuloendotheliosis virus long terminal repeat into a bacterial artificial chromosome clone of Marek’s disease virus (MDV) alters expression of nearby MDV genes

Researchers reported that co-cultivating the JM/102W strain of Marek's disease virus (MDV) with reticuloendotheliosis virus (REV) resulted in an REV long terminal repeat (LTR) being inserted into the internal repeat short (IRS) region of JM/102W. When the resulting recombinant virus was serially passed in cell culture, the initial LTR was duplicated and a second LTR spontaneously appeared in the terminal repeat short (TRS) region of the MDV genome. The virus, designated RM1, was significantly attenuated but still induced severe bursal and thymic atrophy (Isfort et al. PNAS 89:991-995). To determine whether the altered phenotype was due solely to the LTR, we cloned the LTR from the RM1 IRS region and inserted it into the IRS region of a very virulent bacterial artificial clone (BAC) of the Md5 strain of MDV, which we designated rMd5-RM1-LTR. During blind passage in duck embryo fibroblast cultures, the initial LTR in the rMd5-RM1-LTR was also duplicated, with LTRs appearing in both IRS and TRS regions of the MDV genome. The inserted LTR sequences and transcripts associated with the MDV open reading frames MDV085, MDV086, SORF2, US1, and US10 were molecularly characterized. The parental Md5 BAC contains a family of transcripts of 3, 2, and 1kb that all terminate at the end of the US10 gene. The rMd5-RM1-LTR and RM1 viruses both express an additional 4kb transcript that originates in the LTR and also terminates after US10. Collectively, the data suggest that our engineered rMd5-RM1-LTR virus very closely resembles the RM1 virus in its structure and transcription patterns.

Independent duplications of α-amylase in different strains of Aspergillus oryzae

Aspergillus oryzae is a filamentous fungus that has arisen through the ancient domestication of Aspergillus flavus for making traditional oriental foods and beverages. In the many centuries A. oryzae has been used for fermenting the starch in rice to simple sugars, it has undergone selection for increased secretion of starch-degrading enzymes. In particular, all A. oryzae strains investigated thus far have two or more copies of a gene encoding α-amylase, whereas A. flavus has only one. Here we investigate the duplications leading to these copies in three A. oryzae strains. We find evidence of at least three separate duplications of α-amylase, an example of parallel evolution in a micro-organism under artificial selection. At least two of these duplications appear to be associated with activity of transposable elements of the Tc1/mariner class. Both involve a 9.1 kb element that terminates in inverted repeats, encodes a putative transposase and another putative protein of unknown function, and contains an unusual arrangement of four short internal imperfect repeats. Although “unusual Mariners” of this size have previously been identified in A. oryzae, Aspergillus fumigatus and Aspergillus nidulans, this is the first evidence we know of that at least some of them are active in modern times and that their activity can contribute to beneficial genetic changes.