Journal articles: 'Polycistronic gene'

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Gallaher, Sean D., Rory J. Craig, Iniyan Ganesan, Samuel O. Purvine, Sean R. McCorkle, Jane Grimwood, Daniela Strenkert, et al. "Widespread polycistronic gene expression in green algae." Proceedings of the National Academy of Sciences 118, no. 7 (February 12, 2021): e2017714118. http://dx.doi.org/10.1073/pnas.2017714118.

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Polycistronic gene expression, common in prokaryotes, was thought to be extremely rare in eukaryotes. The development of long-read sequencing of full-length transcript isomers (Iso-Seq) has facilitated a reexamination of that dogma. Using Iso-Seq, we discovered hundreds of examples of polycistronic expression of nuclear genes in two divergent species of green algae: Chlamydomonas reinhardtii and Chromochloris zofingiensis. Here, we employ a range of independent approaches to validate that multiple proteins are translated from a common transcript for hundreds of loci. A chromatin immunoprecipitation analysis using trimethylation of lysine 4 on histone H3 marks confirmed that transcription begins exclusively at the upstream gene. Quantification of polyadenylated [poly(A)] tails and poly(A) signal sequences confirmed that transcription ends exclusively after the downstream gene. Coexpression analysis found nearly perfect correlation for open reading frames (ORFs) within polycistronic loci, consistent with expression in a shared transcript. For many polycistronic loci, terminal peptides from both ORFs were identified from proteomics datasets, consistent with independent translation. Synthetic polycistronic gene pairs were transcribed and translated in vitro to recapitulate the production of two distinct proteins from a common transcript. The relative abundance of these two proteins can be modified by altering the Kozak-like sequence of the upstream gene. Replacement of the ORFs with selectable markers or reporters allows production of such heterologous proteins, speaking to utility in synthetic biology approaches. Conservation of a significant number of polycistronic gene pairs between C. reinhardtii, C. zofingiensis, and five other species suggests that this mechanism may be evolutionarily ancient and biologically important in the green algal lineage.

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Blumenthal, Thomas. "Gene clusters and polycistronic transcription in eukaryotes." BioEssays 20, no. 6 (December 6, 1998): 480–87. http://dx.doi.org/10.1002/(sici)1521-1878(199806)20:6<480::aid-bies6>3.0.co;2-q.

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Wong, S., T. H. Morales, J. E. Neigel, and D. A. Campbell. "Genomic and transcriptional linkage of the genes for calmodulin, EF-hand 5 protein, and ubiquitin extension protein 52 in Trypanosoma brucei." Molecular and Cellular Biology 13, no. 1 (January 1993): 207–16. http://dx.doi.org/10.1128/mcb.13.1.207-216.1993.

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We report genomic linkage of a pair of tandem, identical ubiquitin-extension protein 52 (EP52) genes, a novel EF-hand superfamily member gene (EFH5), and the calmodulin gene cluster in Trypanosoma brucei. The intergenic regions of these four genes are short: about 108 bp between the calmodulin gene C and the EFH5 gene, about 111 bp between the EFH5 gene and the ubiquitin-EP52/1 gene, and about 116 bp between the ubiquitin-EP52/1 and -EP52/2 genes. RNA molecules that span these three intergenic regions have been detected by polymerase chain reaction, which suggests that the genes are transcribed in a polycistronic manner. Transcription of the calmodulin, EFH5, and ubiquitin-EP52 genes in isolated nuclei is rapidly inactivated by UV irradiation, which further strengthens the hypothesis that this cluster of three different genes is transcribed in a polycistronic manner and suggests that they are under the control of a single distant upstream promoter. These results suggest that polycistronic transcription is common in trypanosomes and will probably be found for most, if not all, protein-encoding genes. The presence of at least three housekeeping genes with different known or potential regulatory functions within a polycistronic unit suggests that regulation of transcription initiation plays an important role in the coordinated expression of housekeeping genes in trypanosomes.

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Wong, S., T. H. Morales, J. E. Neigel, and D. A. Campbell. "Genomic and transcriptional linkage of the genes for calmodulin, EF-hand 5 protein, and ubiquitin extension protein 52 in Trypanosoma brucei." Molecular and Cellular Biology 13, no. 1 (January 1993): 207–16. http://dx.doi.org/10.1128/mcb.13.1.207.

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We report genomic linkage of a pair of tandem, identical ubiquitin-extension protein 52 (EP52) genes, a novel EF-hand superfamily member gene (EFH5), and the calmodulin gene cluster in Trypanosoma brucei. The intergenic regions of these four genes are short: about 108 bp between the calmodulin gene C and the EFH5 gene, about 111 bp between the EFH5 gene and the ubiquitin-EP52/1 gene, and about 116 bp between the ubiquitin-EP52/1 and -EP52/2 genes. RNA molecules that span these three intergenic regions have been detected by polymerase chain reaction, which suggests that the genes are transcribed in a polycistronic manner. Transcription of the calmodulin, EFH5, and ubiquitin-EP52 genes in isolated nuclei is rapidly inactivated by UV irradiation, which further strengthens the hypothesis that this cluster of three different genes is transcribed in a polycistronic manner and suggests that they are under the control of a single distant upstream promoter. These results suggest that polycistronic transcription is common in trypanosomes and will probably be found for most, if not all, protein-encoding genes. The presence of at least three housekeeping genes with different known or potential regulatory functions within a polycistronic unit suggests that regulation of transcription initiation plays an important role in the coordinated expression of housekeeping genes in trypanosomes.

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Chen, Yiwei, Liji Cao, Chonglin Luo, Désirée AW Ditzel, Jörg Peter, and Rolf Sprengel. "RANGE: Gene Transfer of Reversibly Controlled Polycistronic Genes." Molecular Therapy - Nucleic Acids 2 (2013): e85. http://dx.doi.org/10.1038/mtna.2013.15.

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Berberof, M., A. Pays, and E. Pays. "A similar gene is shared by both the variant surface glycoprotein and procyclin gene transcription units of Trypanosoma brucei." Molecular and Cellular Biology 11, no. 3 (March 1991): 1473–79. http://dx.doi.org/10.1128/mcb.11.3.1473-1479.1991.

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The genes for the variant surface glycoprotein (VSG) and procyclin are expressed in a mutually exclusive manner during the life cycle of Trypanosoma brucei and synthesize the most abundant mRNAs specific to the bloodstream and procyclic stages of the parasite, respectively. Genes belonging to the polycistronic transcription unit of the VSG gene (expression site-associated genes [ESAGs]) are uniquely expressed in the bloodstream form, but some members of ESAG families (genes related to ESAGs [GRESAGs]) are independently transcribed outside the VSG gene expression site. We report here that a gene related to ESAG 2, GRESAG 2.1, is present and expressed in a procyclin gene transcription unit (PARP A locus), which is polycistronic. Members of the ESAG 2 family are thus present in the two major differentially stage-regulated transcription units of this parasite.

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Berberof, M., A. Pays, and E. Pays. "A similar gene is shared by both the variant surface glycoprotein and procyclin gene transcription units of Trypanosoma brucei." Molecular and Cellular Biology 11, no. 3 (March 1991): 1473–79. http://dx.doi.org/10.1128/mcb.11.3.1473.

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The genes for the variant surface glycoprotein (VSG) and procyclin are expressed in a mutually exclusive manner during the life cycle of Trypanosoma brucei and synthesize the most abundant mRNAs specific to the bloodstream and procyclic stages of the parasite, respectively. Genes belonging to the polycistronic transcription unit of the VSG gene (expression site-associated genes [ESAGs]) are uniquely expressed in the bloodstream form, but some members of ESAG families (genes related to ESAGs [GRESAGs]) are independently transcribed outside the VSG gene expression site. We report here that a gene related to ESAG 2, GRESAG 2.1, is present and expressed in a procyclin gene transcription unit (PARP A locus), which is polycistronic. Members of the ESAG 2 family are thus present in the two major differentially stage-regulated transcription units of this parasite.

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8

De Gaudenzi, Javier G., Griselda Noé, Vanina A. Campo, Alberto C. Frasch, and Alejandro Cassola. "Gene expression regulation in trypanosomatids." Essays in Biochemistry 51 (October 24, 2011): 31–46. http://dx.doi.org/10.1042/bse0510031.

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Trypanosomatids are protozoan micro-organisms that cause serious health problems in humans and domestic animals. In addition to their medical relevance, these pathogens have novel biological structures and processes. From nuclear DNA transcription to mRNA translation, trypanosomes use unusual mechanisms to control gene expression. For example, transcription by RNAPII (RNA polymerase II) is polycistronic, and only a few transcription initiation sites have been identified so far. The sequences present in the polycistronic units code for proteins having unrelated functions, that is, not involved in a similar metabolic pathway. Owing to these biological constraints, these micro-organisms regulate gene expression mostly by post-transcriptional events. Consequently, the function of proteins that recognize RNA elements preferentially at the 3′ UTR (untranslated region) of transcripts is central. It was recently shown that mRNP (messenger ribonucleoprotein) complexes are organized within post-transcriptional operons to co-ordinately regulate gene expression of functionally linked transcripts. In the present chapter we will focus on particular characteristics of gene expression in the so-called TriTryp parasites: Trypanosoma cruzi, Trypanosoma brucei and Leishmania major.

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9

Marco, Antonio, Maria Ninova, and Sam Griffiths-Jones. "Multiple products from microRNA transcripts." Biochemical Society Transactions 41, no. 4 (July 18, 2013): 850–54. http://dx.doi.org/10.1042/bst20130035.

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A single transcript sometimes codes for more than one product. In bacteria, and in a few exceptional animal lineages, many genes are organized into operons: clusters of open reading frames that are transcribed together in a single polycistronic transcript. However, polycistronic transcripts are rare in eukaryotes. One notable exception is that of miRNAs (microRNAs), small RNAs that regulate gene expression at the post-transcriptional level. The primary transcripts of miRNAs commonly produce more than one functional product, by at least three different mechanisms. miRNAs are often produced from polycistronic transcripts together with other miRNA precursors. Also, miRNAs frequently derive from protein-coding gene introns. Finally, each miRNA precursor can produce two mature miRNA products. We argue, in the present review, that miRNAs are frequently hosted in transcripts coding for multiple products because new miRNA precursor sequences that arise by chance in transcribed regions are more likely to become functional miRNAs during evolution.

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Reynolds, David, Laura Cliffe, Konrad U. Förstner, Chung-Chau Hon, T. Nicolai Siegel, and Robert Sabatini. "Regulation of transcription termination by glucosylated hydroxymethyluracil, base J, in Leishmania major and Trypanosoma brucei." Nucleic Acids Research 42, no. 15 (August 7, 2014): 9717–29. http://dx.doi.org/10.1093/nar/gku714.

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Abstract Base J, β-d-glucosyl-hydroxymethyluracil, is an epigenetic modification of thymine in the nuclear DNA of flagellated protozoa of the order Kinetoplastida. J is enriched at sites involved in RNA polymerase (RNAP) II initiation and termination. Reduction of J in Leishmania tarentolae via growth in BrdU resulted in cell death and indicated a role of J in the regulation of RNAP II termination. To further explore J function in RNAP II termination among kinetoplastids and avoid indirect effects associated with BrdU toxicity and genetic deletions, we inhibited J synthesis in Leishmania major and Trypanosoma brucei using DMOG. Reduction of J in L. major resulted in genome-wide defects in transcription termination at the end of polycistronic gene clusters and the generation of antisense RNAs, without cell death. In contrast, loss of J in T. brucei did not lead to genome-wide termination defects; however, the loss of J at specific sites within polycistronic gene clusters led to altered transcription termination and increased expression of downstream genes. Thus, J regulation of RNAP II transcription termination genome-wide is restricted to Leishmania spp., while in T. brucei it regulates termination and gene expression at specific sites within polycistronic gene clusters.

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11

Qu, Liang-Hu, Anthony Henras, Yong-Jun Lu, Hui Zhou, Wei-xin Zhou, Yuan-Qi Zhu, Jin Zhao, Yves Henry, Michèle Caizergues-Ferrer, and Jean-Pierre Bachellerie. "Seven Novel Methylation Guide Small Nucleolar RNAs Are Processed from a Common Polycistronic Transcript by Rat1p and RNase III in Yeast." Molecular and Cellular Biology 19, no. 2 (February 1, 1999): 1144–58. http://dx.doi.org/10.1128/mcb.19.2.1144.

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ABSTRACT Through a computer search of the genome of the yeastSaccharomyces cerevisiae, the coding sequences of seven different box C/D antisense small nucleolar RNAs (snoRNAs) with the structural hallmarks of guides for rRNA ribose methylation have been detected clustered over a 1.4-kb tract in an inter-open reading frame region of chromosome XIII. The corresponding snoRNAs have been positively identified in yeast cells. Disruption of the nonessential snoRNA gene cluster specifically suppressed the seven cognate rRNA ribose methylations but did not result in any growth delay under the conditions of yeast culture tested. The seven snoRNAs are processed from a common polycistronic transcript synthesized from an independent promoter, similar to some plant snoRNAs but in marked contrast with their vertebrate functional homologues processed from pre-mRNA introns containing a single snoRNA. Processing of the polycistronic precursor requires nucleases also involved in rRNA processing, i.e., Rnt1p and Rat1p. After disruption of the RNT1 gene, the yeast ortholog of bacterial RNase III, production of the seven mature snoRNAs was abolished, while the polycistronic snoRNA precursor accumulated. In cells lacking functional Rat1p, an exonuclease involved in the processing of both pre-rRNA and intron-encoded snoRNAs, several processing intermediates of the polycistronic precursor accumulated. This allowed for the mapping in the precursor of the presumptive Rnt1p endonucleolytic cuts which provide entry sites for subsequent exonucleolytic trimming of the pre-snoRNAs. In line with known properties of double-stranded RNA-specific RNase III, pairs of Rnt1p cuts map next to each other on opposite strands of long double-helical stems in the secondary structure predicted for the polycistronic snoRNA precursor.

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12

Hecht, Katrin, James E. Bailey, and Wolfgang Minas. "Polycistronic gene expression in yeast versus cryptic promoter elements." FEMS Yeast Research 2, no. 2 (May 2002): 215–24. http://dx.doi.org/10.1111/j.1567-1364.2002.tb00086.x.

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HECHT, K., J. BAILEY, and W. MINAS. "Polycistronic gene expression in yeast versus cryptic promoter elements." FEMS Yeast Research 2, no. 2 (May 2002): 215–24. http://dx.doi.org/10.1016/s1567-1356(02)00085-5.

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Alexander, Dylan C., Michael J. Brumlik, Linda Lee, and Susan E. Jensen. "Early Cephamycin Biosynthetic Genes Are Expressed from a Polycistronic Transcript in Streptomyces clavuligerus." Journal of Bacteriology 182, no. 2 (January 15, 2000): 348–56. http://dx.doi.org/10.1128/jb.182.2.348-356.2000.

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ABSTRACT A polycistronic transcript that is initiated at the latpromoter has been implicated in the expression of the genes involved in early steps of cephamycin C biosynthesis in Streptomyces clavuligerus. pcbC is also expressed as a monocistronic transcript from its own promoter. However, an alternative interpretation involving expression via three separate yet interdependent transcripts has also been proposed. To distinguish between these possibilities, mutants lacking the latpromoter and containing a transcription terminator within thelat gene (Δlat::tsr/term mutants) were created. This mutation eliminated the production of lysine-ɛ-aminotransferase (the lat gene product) but also affected the expression of downstream genes, indicating an operon arrangement. Production of δ-(l-α-aminoadipyl)-l-cysteinyl-d-valine synthetase (ACVS) (the pcbAB gene product) was eliminated in Δlat::tsr/term mutants, while production of isopenicillin N synthase (IPNS) (the pcbCgene product) was greatly reduced. The provision of α-aminoadipate to the Δlat::tsr/term mutants, either via exogenous feeding or via lat gene complementation, did not restore production of ACVS or IPNS. Analysis of RNA isolated from the Δlat::tsr/term mutants confirmed that the polycistronic transcript was absent but also indicated that monocistronic pcbC transcript levels were greatly decreased. In contrast, Δlat mutants created by in-frame internal deletion of lat maintained the polycistronic transcript and allowed production of wild-type levels of both ACVS and IPNS.

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Reeves, Andrew R., R. Samuel English, J. S. Lampel, David A. Post, and Thomas J. Vanden Boom. "Transcriptional Organization of the Erythromycin Biosynthetic Gene Cluster of Saccharopolyspora erythraea." Journal of Bacteriology 181, no. 22 (November 15, 1999): 7098–106. http://dx.doi.org/10.1128/jb.181.22.7098-7106.1999.

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ABSTRACT The transcriptional organization of the erythromycin biosynthetic gene (ery) cluster of Saccharopolyspora erythraea has been examined by a variety of methods, including S1 nuclease protection assays, Northern blotting, Western blotting, and bioconversion analysis of erythromycin intermediates. The analysis was facilitated by the construction of novel mutants containing a S. erythraea transcriptional terminator within theeryAI, eryAIII, eryBIII,eryBIV, eryBV, eryBVI,eryCIV, and eryCVI genes and additionally by aneryAI −10 promoter mutant. All mutant strains demonstrated polar effects on the transcription of downstream erybiosynthetic genes. Our results demonstrate that the erygene cluster contains four major polycistronic transcriptional units, the largest one extending approximately 35 kb from eryAI toeryG. Two overlapping polycistronic transcripts extending from eryBIV to eryBVII were identified. In addition, seven ery cluster promoter transcription start sites, one each beginning at eryAI, eryBI,eryBIII, eryBVI, and eryK and two beginning at eryBIV, were determined.

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Padilla-Mejía, Norma E., Luis E. Florencio-Martínez, Rodrigo Moreno-Campos, Juan C. Vizuet-de-Rueda, Ana M. Cevallos, Rosaura Hernández-Rivas, Rebeca Manning-Cela, and Santiago Martínez-Calvillo. "The Selenocysteine tRNA Gene in Leishmania major Is Transcribed by both RNA Polymerase II and RNA Polymerase III." Eukaryotic Cell 14, no. 3 (December 29, 2014): 216–27. http://dx.doi.org/10.1128/ec.00239-14.

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ABSTRACT Eukaryotic tRNAs, transcribed by RNA polymerase III (Pol III), contain boxes A and B as internal promoter elements. One exception is the selenocysteine (Sec) tRNA (tRNA-Sec), whose transcription is directed by an internal box B and three extragenic sequences in vertebrates. Here we report on the transcriptional analysis of the tRNA-Sec gene in the protozoan parasite Leishmania major . This organism has unusual mechanisms of gene expression, including Pol II polycistronic transcription and maturation of mRNAs by trans splicing, a process that attaches a 39-nucleotide miniexon to the 5′ end of all the mRNAs. In L. major , tRNA-Sec is encoded by a single gene inserted into a Pol II polycistronic unit, in contrast to most tRNAs, which are clustered at the boundaries of polycistronic units. 5′ rapid amplification of cDNA ends and reverse transcription-PCR experiments showed that some tRNA-Sec transcripts contain the miniexon at the 5′ end and a poly(A) tail at the 3′ end, indicating that the tRNA-Sec gene is polycistronically transcribed by Pol II and processed by trans splicing and polyadenylation, as was recently reported for the tRNA-Sec genes in the related parasite Trypanosoma brucei . However, nuclear run-on assays with RNA polymerase inhibitors and with cells that were previously UV irradiated showed that the tRNA-Sec gene in L. major is also transcribed by Pol III. Thus, our results indicate that RNA polymerase specificity in Leishmania is not absolute in vivo , as has recently been found in other eukaryotes.

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Remm, Maido, Anu Remm, and Mart Ustav. "Human Papillomavirus Type 18 E1 Protein Is Translated from Polycistronic mRNA by a Discontinuous Scanning Mechanism." Journal of Virology 73, no. 4 (April 1, 1999): 3062–70. http://dx.doi.org/10.1128/jvi.73.4.3062-3070.1999.

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ABSTRACT Papillomaviruses are small double-stranded DNA viruses that replicate episomally in the nuclei of infected cells. The full-length E1 protein of papillomaviruses is required for the replication of viral DNA. The viral mRNA from which the human papillomavirus type 18 E1 protein is expressed is not known. We demonstrate that in eukaryotic cells, the E1 protein is expressed from polycistronic mRNA containing E6, E7, and E1 open reading frames (ORFs). The translation of adjacent E7 and E1 ORFs is not associated; it is performed by separate populations of ribosomes. The translation of the downstream E1 gene is preceded by ribosome scanning. Scanning happens at least at the 5′ end of the polycistronic mRNA and also approximately 100 bp in front of the E1 gene. Long areas in middle of the mRNA are bypassed by ribosomes, possibly by ribosomal “shunting.” Inactivation of short minicistrons in the upstream area of the E1 gene did not change the expression level of the E1 gene.

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Rui fang, Li, Wang Bin, Yi Yan jie, Huang Liang, and Xiong Qian cheng. "Polycistronic expression of CGA-N46 gene in Bacillus subtilis DB1342." African Journal of Microbiology Research 7, no. 26 (June 25, 2013): 3294–303. http://dx.doi.org/10.5897/ajmr10.796.

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Wiznerowicz, M., A. C. Fong, P. Wysocki, A. Mackiewicz, and R. G. Hawley. "Polycistronic retroviral vectors for immuno-gene therapy of human melanoma." Immunology Letters 56 (May 1997): 164. http://dx.doi.org/10.1016/s0165-2478(97)85656-8.

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Wiznerowicz, M. "Polycistronic retroviral vectors for immuno-gene therapy of human melanoma." Immunology Letters 56, no. 1-3 (May 1997): 164. http://dx.doi.org/10.1016/s0165-2478(97)87494-9.

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21

Clayton, Christine. "Regulation of gene expression in trypanosomatids: living with polycistronic transcription." Open Biology 9, no. 6 (June 2019): 190072. http://dx.doi.org/10.1098/rsob.190072.

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In trypanosomes, RNA polymerase II transcription is polycistronic and individual mRNAs are excised by trans -splicing and polyadenylation. The lack of individual gene transcription control is compensated by control of mRNA processing, translation and degradation. Although the basic mechanisms of mRNA decay and translation are evolutionarily conserved, there are also unique aspects, such as the existence of six cap-binding translation initiation factor homologues, a novel decapping enzyme and an mRNA stabilizing complex that is recruited by RNA-binding proteins. High-throughput analyses have identified nearly a hundred regulatory mRNA-binding proteins, making trypanosomes valuable as a model system to investigate post-transcriptional regulation.

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Rudenko, G., S. Le Blancq, J. Smith, M. G. Lee, A. Rattray, and L. H. Van der Ploeg. "Procyclic acidic repetitive protein (PARP) genes located in an unusually small alpha-amanitin-resistant transcription unit: PARP promoter activity assayed by transient DNA transfection of Trypanosoma brucei." Molecular and Cellular Biology 10, no. 7 (July 1990): 3492–504. http://dx.doi.org/10.1128/mcb.10.7.3492-3504.1990.

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At least one of the procyclic acidic repetitive protein (PARP or procyclin) loci of Trypanosoma brucei is a small (5- to 6-kilobase) polycistronic transcription unit which is transcribed in an alpha-amanitin-resistant manner. Its single promoter, as mapped by run-on transcription analysis and UV inactivation of transcription, is located immediately upstream of the first alpha-PARP gene. Transcription termination occurs in a region approximately 3 kilobases downstream of the beta-PARP gene. The location of the promoter was confirmed by its ability to direct transcription of the bacterial chloramphenicol acetyltransferase gene in insect-form (procyclic) T. brucei. The putative PARP promoter is located in the region between the 3' splice acceptor site (nucleotide position 0) and nucleotide position -196 upstream of the alpha-PARP genes. Regulatory regions influencing the levels of PARP expression may be located further upstream. We conclude that a single promoter, which is located very close to the 3' splice acceptor site of the alpha-PARP genes, directs the transcription of a small, polycistronic, and alpha-amanitin-resistant transcription unit.

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Rudenko, G., S. Le Blancq, J. Smith, M. G. Lee, A. Rattray, and L. H. Van der Ploeg. "Procyclic acidic repetitive protein (PARP) genes located in an unusually small alpha-amanitin-resistant transcription unit: PARP promoter activity assayed by transient DNA transfection of Trypanosoma brucei." Molecular and Cellular Biology 10, no. 7 (July 1990): 3492–504. http://dx.doi.org/10.1128/mcb.10.7.3492.

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At least one of the procyclic acidic repetitive protein (PARP or procyclin) loci of Trypanosoma brucei is a small (5- to 6-kilobase) polycistronic transcription unit which is transcribed in an alpha-amanitin-resistant manner. Its single promoter, as mapped by run-on transcription analysis and UV inactivation of transcription, is located immediately upstream of the first alpha-PARP gene. Transcription termination occurs in a region approximately 3 kilobases downstream of the beta-PARP gene. The location of the promoter was confirmed by its ability to direct transcription of the bacterial chloramphenicol acetyltransferase gene in insect-form (procyclic) T. brucei. The putative PARP promoter is located in the region between the 3' splice acceptor site (nucleotide position 0) and nucleotide position -196 upstream of the alpha-PARP genes. Regulatory regions influencing the levels of PARP expression may be located further upstream. We conclude that a single promoter, which is located very close to the 3' splice acceptor site of the alpha-PARP genes, directs the transcription of a small, polycistronic, and alpha-amanitin-resistant transcription unit.

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Evers, Raymond, and Albert W. C. A. Cornelissen. "TheTrypanosoma bruceiprotein phosphatase gene: polycistronic transcription with the RNA polymerase II largest subunit gene." Nucleic Acids Research 18, no. 17 (1990): 5089–95. http://dx.doi.org/10.1093/nar/18.17.5089.

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Tombácz, Dóra, István Prazsák, Gábor Torma, Zsolt Csabai, Zsolt Balázs, Norbert Moldován, Béla Dénes, Michael Snyder, and Zsolt Boldogkői. "Time-Course Transcriptome Profiling of a Poxvirus Using Long-Read Full-Length Assay." Pathogens 10, no. 8 (July 21, 2021): 919. http://dx.doi.org/10.3390/pathogens10080919.

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Viral transcriptomes that are determined using first- and second-generation sequencing techniques are incomplete. Due to the short read length, these methods are inefficient or fail to distinguish between transcript isoforms, polycistronic RNAs, and transcriptional overlaps and readthroughs. Additionally, these approaches are insensitive for the identification of splice and transcriptional start sites (TSSs) and, in most cases, transcriptional end sites (TESs), especially in transcript isoforms with varying transcript ends, and in multi-spliced transcripts. Long-read sequencing is able to read full-length nucleic acids and can therefore be used to assemble complete transcriptome atlases. Although vaccinia virus (VACV) does not produce spliced RNAs, its transcriptome has a high diversity of TSSs and TESs, and a high degree of polycistronism that leads to enormous complexity. We applied single-molecule, real-time, and nanopore-based sequencing methods to investigate the time-lapse transcriptome patterns of VACV gene expression.

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Barbet, Anthony F., Anna Lundgren, Jooyoung Yi, Fred R. Rurangirwa, and Guy H. Palmer. "Antigenic Variation of Anaplasma marginale by Expression of MSP2 Mosaics." Infection and Immunity 68, no. 11 (November 1, 2000): 6133–38. http://dx.doi.org/10.1128/iai.68.11.6133-6138.2000.

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ABSTRACT Anaplasma marginale is a tick-borne pathogen, one of several closely related ehrlichial organisms that cause disease in animals and humans. These Ehrlichia species have complex life cycles that require, in addition to replication and development within the tick vector, evasion of the immune system in order to persist in the mammalian reservoir host. This complexity requires efficient use of the small ehrlichial genome. A. marginaleand related ehrlichiae express immunoprotective, variable outer membrane proteins that have similar structures and are encoded by polymorphic multigene families. We show here that the major outer membrane protein of A. marginale, MSP2, is encoded on a polycistronic mRNA. The genomic expression site for this mRNA is polymorphic and encodes numerous amino acid sequence variants in bloodstream populations of A. marginale. A potential mechanism for persistence is segmental gene conversion of the expression site to link hypervariable msp2 sequences to the promoter and polycistron.

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Miki, Takashi S., Sarah H. Carl, Michael B. Stadler, and Helge Großhans. "XRN2 Autoregulation and Control of Polycistronic Gene Expresssion in Caenorhabditis elegans." PLOS Genetics 12, no. 9 (September 15, 2016): e1006313. http://dx.doi.org/10.1371/journal.pgen.1006313.

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Reiss, Jochen, Nadine Cohen, Claude Dorche, Hanna Mandel, Ralf R. Mendel, Birgit Stallmeyer, Marie-Therese Zabot, and Thomas Dierks. "Mutations in a polycistronic nuclear gene associated with molybdenum cofactor deficiency." Nature Genetics 20, no. 1 (September 1998): 51–53. http://dx.doi.org/10.1038/1706.

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Beauchemin, M., S. Roy, P. Daoust, S. Dagenais-Bellefeuille, T. Bertomeu, L. Letourneau, B. F. Lang, and D. Morse. "Dinoflagellate tandem array gene transcripts are highly conserved and not polycistronic." Proceedings of the National Academy of Sciences 109, no. 39 (September 10, 2012): 15793–98. http://dx.doi.org/10.1073/pnas.1206683109.

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Newbury, Sarah F., Noel H. Smith, and Christopher F. Higgins. "Differential mRNA stability controls relative gene expression within a polycistronic operon." Cell 51, no. 6 (December 1987): 1131–43. http://dx.doi.org/10.1016/0092-8674(87)90599-x.

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Enguita, Francisco J., Juan Jose R. Coque, Paloma Liras, and Juan F. Martin. "The Nine Genes of the Nocardia lactamdurans Cephamycin Cluster Are Transcribed into Large mRNAs from Three Promoters, Two of Them Located in a Bidirectional Promoter Region." Journal of Bacteriology 180, no. 20 (October 15, 1998): 5489–94. http://dx.doi.org/10.1128/jb.180.20.5489-5494.1998.

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ABSTRACT The nine biosynthesis genes of the Nocardia lactamdurans cephamycin cluster are expressed as three different mRNAs initiating at promoters latp, cefDp, andpcbABp, as shown by low-resolution S1 nuclease protection assays and Northern blotting analysis. Bidirectional expression occurred from divergent promoters (latp andcefDp) located in a 629-bp intergenic region that contains three heptameric direct repeats similar to those recognized by members of the SARP (Streptomyces antibiotic regulatory proteins) family. The lat gene is transcribed in a single monocistronic transcript initiating at latp. A second unusually long polycistronic mRNA (more than 16 kb) corresponding to six biosynthesis genes (pcbAB, pcbC,cmcI, cmcJ, cefF, andcmcH) started at pcbABp. A third polycistronic mRNA corresponding to the cefD and cefE genes started at cefDp.

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Zhu, Xinwen, Chiara Ricci-Tam, Emily R. Hager, and Allyson E. Sgro. "Self-cleaving peptides for expression of multiple genes in Dictyostelium discoideum." PLOS ONE 18, no. 3 (March 2, 2023): e0281211. http://dx.doi.org/10.1371/journal.pone.0281211.

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The social amoeba Dictyostelium discoideum is a model for a wide range of biological processes including chemotaxis, cell-cell communication, phagocytosis, and development. Interrogating these processes with modern genetic tools often requires the expression of multiple transgenes. While it is possible to transfect multiple transcriptional units, the use of separate promoters and terminators for each gene leads to large plasmid sizes and possible interference between units. In many eukaryotic systems this challenge has been addressed through polycistronic expression mediated by 2A viral peptides, permitting efficient, co-regulated gene expression. Here, we screen the most commonly used 2A peptides, porcine teschovirus-1 2A (P2A), Thosea asigna virus 2A (T2A), equine rhinitis A virus 2A (E2A), and foot-and-mouth disease virus 2A (F2A), for activity in D. discoideum and find that all the screened 2A sequences are effective. However, combining the coding sequences of two proteins into a single transcript leads to notable strain-dependent decreases in expression level, suggesting additional factors regulate gene expression in D. discoideum that merit further investigation. Our results show that P2A is the optimal sequence for polycistronic expression in D. discoideum, opening up new possibilities for genetic engineering in this model system.

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Kelly, S., S. Kramer, A. Schwede, P. K. Maini, K. Gull, and M. Carrington. "Genome organization is a major component of gene expression control in response to stress and during the cell division cycle in trypanosomes." Open Biology 2, no. 4 (April 2012): 120033. http://dx.doi.org/10.1098/rsob.120033.

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The trypanosome genome is characterized by RNA polymerase II-driven polycistronic transcription of protein-coding genes. Ten to hundreds of genes are co-transcribed from a single promoter; thus, selective regulation of individual genes via initiation is impossible. However, selective responses to external stimuli occur and post-transcriptional mechanisms are thought to account for all temporal gene expression patterns. We show that genes encoding mRNAs that are differentially regulated during the heat-shock response are selectively positioned in polycistronic transcription units; downregulated genes are close to transcription initiation sites and upregulated genes are distant. We demonstrate that the position of a reporter gene within a transcription unit is sufficient to reproduce this effect. Analysis of gene ontology annotations reveals that positional bias is not restricted to stress–response genes and that there is a genome-wide organization based on proximity to transcription initiation sites. Furthermore, we show that the relative abundance of mRNAs at different time points in the cell division cycle is dependent on the location of the corresponding genes to transcription initiation sites. This work provides evidence that the genome in trypanosomes is organized to facilitate co-coordinated temporal control of gene expression in the absence of selective promoters.

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Clement, Sandra L., Melissa K. Mingler, and Donna J. Koslowsky. "An Intragenic Guide RNA Location Suggests a Complex Mechanism for Mitochondrial Gene Expression in Trypanosoma brucei." Eukaryotic Cell 3, no. 4 (August 2004): 862–69. http://dx.doi.org/10.1128/ec.3.4.862-869.2004.

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ABSTRACT In Trypanosoma brucei, two classes of transcripts are produced from two distinct mitochondrial genome components. Guide RNAs (gRNAs) are usually minicircle encoded and exist as primary transcripts, while the maxicircle-encoded rRNAs and mRNAs are processed from a polycistronic precursor. The genes for the gRNAs gMURF2-II and gCYb(560) each have uncommon kinetoplast DNA (kDNA) locations that are not typically associated with transcription initiation events. We demonstrate that the conserved maxicircle gRNA gMURF2-II has an unusual location within the ND4 gene. This is the first report of a completely intragenic gene in kDNA. In addition, the gMURF2-II and ND4 transcripts are generated by distinctly different events; the ND4 mRNA is processed from a polycistronic precursor, while transcription of the gRNA initiates downstream of the 5′ end of the ND4 gene. The gCYb(560) gene has an atypical minicircle location in that it is not flanked by the inverted repeat sequences that surround the majority of minicircle gRNA genes. Our data indicate that the mature gCYb(560) gRNA is also a primary transcript and that the 5′-end heterogeneity previously observed for this gRNA is a result of multiple transcription initiation sites and not of imprecise 5′-end processing. Together, these data indicate that gRNA genes represent individual transcription units, regardless of their genomic context, and suggest a complex mechanism for mitochondrial gene expression in T. brucei.

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Xu, Weijing, Jianqiang Huang, and Stanley N. Cohen. "Autoregulation of AbsB (RNase III) Expression in Streptomyces coelicolor by Endoribonucleolytic Cleavage of absB Operon Transcripts." Journal of Bacteriology 190, no. 15 (June 6, 2008): 5526–30. http://dx.doi.org/10.1128/jb.00558-08.

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ABSTRACT The Streptomyces coelicolor absB gene encodes an RNase III family endoribonuclease and is normally essential for antibiotic biosynthesis. Here we report that AbsB controls its own expression by sequentially and site specifically cleaving stem-loop segments of its polycistronic transcript. Our results demonstrate a ribonucleolytic regulatory role for AbsB in vivo.

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Guardado-Valdivia, Lizeth, Alejandra Chacón-López, Jesús Murillo, Jorge Poveda, José Luis Hernández-Flores, Luis Xoca-Orozco, and Selene Aguilera. "The Pbo Cluster from Pseudomonas syringae pv. Phaseolicola NPS3121 Is Thermoregulated and Required for Phaseolotoxin Biosynthesis." Toxins 13, no. 9 (September 7, 2021): 628. http://dx.doi.org/10.3390/toxins13090628.

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The bean (Phaseolus vulgaris) pathogen Pseudomonas syringae pv. phaseolicola NPS3121 synthesizes phaseolotoxin in a thermoregulated way, with optimum production at 18 °C. Gene PSPPH_4550 was previously shown to be thermoregulated and required for phaseolotoxin biosynthesis. Here, we established that PSPPH_4550 is part of a cluster of 16 genes, the Pbo cluster, included in a genomic island with a limited distribution in P. syringae and unrelated to the possession of the phaseolotoxin biosynthesis cluster. We identified typical non-ribosomal peptide synthetase, and polyketide synthetase domains in several of the pbo deduced products. RT-PCR and the analysis of polar mutants showed that the Pbo cluster is organized in four transcriptional units, including one monocistronic and three polycistronic. Operons pboA and pboO are both essential for phaseolotoxin biosynthesis, while pboK and pboJ only influence the amount of toxin produced. The three polycistronic units were transcribed at high levels at 18 °C but not at 28 °C, whereas gene pboJ was constitutively expressed. Together, our data suggest that the Pbo cluster synthesizes secondary metabolite(s), which could participate in the regulation of phaseolotoxin biosynthesis.

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Spiridonova, V. A., A. S. Akhmanova, V. K. Kagramanova, A. K. E. Köpke, and A. S. Mankin. "Ribosomal protein gene cluster of Halobacterium halobium: nucleotide sequence of the genes coding for S3 and L29 equivalent ribosomal proteins." Canadian Journal of Microbiology 35, no. 1 (January 1, 1989): 153–59. http://dx.doi.org/10.1139/m89-023.

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A 1643 base pair fragment encoding the S3 and L29 equivalent ribosomal proteins has been sequenced from the archaebacterium Halobacterium halobium. The incomplete open reading frame present upstream from the S3 gene encodes a protein homologous to the eubacterial ribosomal protein L22. The initiation codons of the S3 and L29 genes overlap with the termination codons of the upstream genes. A tight physical organization suggests that these genes are transcribed as a polycistronic operon. Peculiarities of the protein structure and gene organization are discussed.Key words: archaebacteria, ribosomal protein, halobacteria, gene structure, evolution.

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Li, Y., and S. Altman. "A specific endoribonuclease, RNase P, affects gene expression of polycistronic operon mRNAs." Proceedings of the National Academy of Sciences 100, no. 23 (October 29, 2003): 13213–18. http://dx.doi.org/10.1073/pnas.2235589100.

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Worthey, E. A. "Leishmania major chromosome 3 contains two long convergent polycistronic gene clusters separated by a tRNA gene." Nucleic Acids Research 31, no. 14 (July 15, 2003): 4201–10. http://dx.doi.org/10.1093/nar/gkg469.

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Worthey, E. A. "Leishmania major chromosome 3 contains two long convergent polycistronic gene clusters separated by a tRNA gene." Nucleic Acids Research 32, no. 22 (December 14, 2004): 6716. http://dx.doi.org/10.1093/nar/gki172.

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41

Huang, Tao, Scott Kuersten, Atul M. Deshpande, John Spieth, Margaret MacMorris, and Thomas Blumenthal. "Intercistronic Region Required for Polycistronic Pre-mRNA Processing in Caenorhabditis elegans." Molecular and Cellular Biology 21, no. 4 (February 15, 2001): 1111–20. http://dx.doi.org/10.1128/mcb.21.4.1111-1120.2001.

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ABSTRACT In Caenorhabditis elegans, polycistronic pre-mRNAs are processed by cleavage and polyadenylation at the 3′ ends of the upstream genes and trans splicing, generally to the specialized spliced leader SL2, at the 5′ ends of the downstream genes. Previous studies have indicated a relationship between these two events in the processing of a heat shock-induced gpd-2–gpd-3polycistronic pre-mRNA. Here, we report mutational analysis of the intercistronic region of this operon by linker scan analysis. Surprisingly, no sequences downstream of the 3′ end were important for 3′-end formation. In contrast, a U-rich (Ur) element located 29 bp downstream of the site of 3′-end formation was shown to be important for downstream mRNA biosynthesis. This ∼20-bp element is sufficient for SL2 trans splicing and mRNA accumulation when transplanted to a heterologous context. Furthermore, when the downstream gene was replaced by a gene from another organism, no loss of trans-splicing specificity was observed, suggesting that the Ur element may be the primary signal required for downstream mRNA processing.

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Ventura, Marco, Ralf Zink, Gerald F. Fitzgerald, and Douwe van Sinderen. "Gene Structure and Transcriptional Organization of the dnaK Operon of Bifidobacterium breve UCC 2003 and Application of the Operon in Bifidobacterial Tracing." Applied and Environmental Microbiology 71, no. 1 (January 2005): 487–500. http://dx.doi.org/10.1128/aem.71.1.487-500.2005.

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ABSTRACT The incorporation and delivery of bifidobacterial strains as probiotic components in many food preparations expose these microorganisms to a multitude of environmental insults, including heat and osmotic stresses. We characterized the dnaK gene region of Bifidobacterium breve UCC 2003. Sequence analysis of the dnaK locus revealed four genes with the organization dnaK-grpE-dnaJ-ORF1, whose deduced protein products display significant similarity to corresponding chaperones found in other bacteria. Northern hybridization and real-time LightCycler PCR analysis revealed that the transcription of the dnaK operon was strongly induced by osmotic shock but was not induced significantly by heat stress. A 4.4-kb polycistronic mRNA, which represented the transcript of the complete dnaK gene region, was detected. Many other small transcripts, which were assumed to have resulted from intensive processing or degradation of this polycistronic mRNA, were identified. The transcription start site of the dnaK operon was determined by primer extension. Phylogenetic analysis of the available bifidobacterial grpE and dnaK genes suggested that the evolutionary development of these genes has been similar. The phylogeny derived from the various bifidobacterial grpE and dnaK sequences is consistent with that derived from 16S rRNA. The use of these genes in bifidobacterial species as an alternative or complement to the 16S rRNA gene marker provides sequence signatures that allow a high level of discrimination between closely related species of this genus.

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Nützmann, Hans-Wilhelm, Claudio Scazzocchio, and Anne Osbourn. "Metabolic Gene Clusters in Eukaryotes." Annual Review of Genetics 52, no. 1 (November 23, 2018): 159–83. http://dx.doi.org/10.1146/annurev-genet-120417-031237.

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In bacteria, more than half of the genes in the genome are organized in operons. In contrast, in eukaryotes, functionally related genes are usually dispersed across the genome. There are, however, numerous examples of functional clusters of nonhomologous genes for metabolic pathways in fungi and plants. Despite superficial similarities with operons (physical clustering, coordinate regulation), these clusters have not usually originated by horizontal gene transfer from bacteria, and (unlike operons) the genes are typically transcribed separately rather than as a single polycistronic message. This clustering phenomenon raises intriguing questions about the origins of clustered metabolic pathways in eukaryotes and the significance of clustering for pathway function. Here we review metabolic gene clusters from fungi and plants, highlight commonalities and differences, and consider how these clusters form and are regulated. We also identify opportunities for future research in the areas of large-scale genomics, synthetic biology, and experimental evolution.

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Kessler, Alexandra, Arie B. Brinkman, John van der Oost, and David Prangishvili. "Transcription of the Rod-Shaped Viruses SIRV1 and SIRV2 of the Hyperthermophilic Archaeon Sulfolobus." Journal of Bacteriology 186, no. 22 (November 15, 2004): 7745–53. http://dx.doi.org/10.1128/jb.186.22.7745-7753.2004.

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ABSTRACT The double-stranded DNA genomes of the crenarchaeal rudiviruses SIRV1 (32 kb) and SIRV2 (35 kb) were previously sequenced. Here we present results of the analysis of gene expression of these viruses at different time points after infection of the host cell, Sulfolobus islandicus, and of the mapping of transcriptional start sites. Transcription of both genomes starts simultaneously at multiple sites spread over the total length of the genome and from both strands. The earliest time point when viral transcripts could be detected in cells was 30 min after infection. At this time point all the viral genes, except one, were transcribed. Many genes were clustered and appeared to be transcribed as polycistronic messengers. Although the coat protein-encoding gene was initially also transcribed as a polycistronic messenger, an abundant monocistronic transcript of this gene was detected 2 to 3 h after infection, just before assembly of viral particles. The expression of a single gene, adjacent to the coat protein gene, was upregulated at the late phase of infection, suggesting that it might be involved in specific processing and activation of the coat protein messenger. Start sites of 13 transcripts from the SIRV1 genome have been mapped by primer extension, and promoter sequences have been identified. Similar to host promoters, these viral promoters all contain potential binding sites for the archaeal transcription factors TATA binding protein and transcription factor B. In addition, most of them contain a virus-specific consensus element, suggesting the involvement of alternative transcription factors.

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Antoine, Rudy, Françoise Jacob-Dubuisson, Hervé Drobecq, Eve Willery, Sarah Lesjean, and Camille Locht. "Overrepresentation of a Gene Family Encoding Extracytoplasmic Solute Receptors in Bordetella." Journal of Bacteriology 185, no. 4 (February 15, 2003): 1470–74. http://dx.doi.org/10.1128/jb.185.4.1470-1474.2003.

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ABSTRACT A family of genes that are likely to encode extracytoplasmic solute receptors is strongly overrepresented in several β-proteobacteria, including Bordetella pertussis. This gene family, of which members have been called bug genes, contains some examples that are contained within polycistronic operons coding for tripartite uptake transporters of the TTT family, while the vast majority are “orphan” genes. Proteomic and functional analyses demonstrated that several of these genes are expressed in B. pertussis, and one is involved in citrate uptake. The bug genes probably form an ancient family that has been subjected to a large expansion in a restricted phylogenic group.

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Martínez-Calvillo, Santiago, Juan C. Vizuet-de-Rueda, Luis E. Florencio-Martínez, Rebeca G. Manning-Cela, and Elisa E. Figueroa-Angulo. "Gene Expression in Trypanosomatid Parasites." Journal of Biomedicine and Biotechnology 2010 (2010): 1–15. http://dx.doi.org/10.1155/2010/525241.

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The parasitesLeishmaniaspp.,Trypanosoma brucei,andTrypanosoma cruziare the trypanosomatid protozoa that cause the deadly human diseases leishmaniasis, African sleeping sickness, and Chagas disease, respectively. These organisms possess unique mechanisms for gene expression such as constitutive polycistronic transcription of protein-coding genes and trans-splicing. Little is known about either the DNA sequences or the proteins that are involved in the initiation and termination of transcription in trypanosomatids.In silicoanalyses of the genome databases of these parasites led to the identification of a small number of proteins involved in gene expression. However, functional studies have revealed that trypanosomatids have more general transcription factors than originally estimated. Many posttranslational histone modifications, histone variants, and chromatin modifying enzymes have been identified in trypanosomatids, and recent genome-wide studies showed that epigenetic regulation might play a very important role in gene expression in this group of parasites. Here, we review and comment on the most recent findings related to transcription initiation and termination in trypanosomatid protozoa.

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Venturini, Letizia, Karin Battmer, Mirco Castoldi, Beate Schultheis, Andreas Hochhaus, Martina U. Muckenthaler, Arnold Ganser, Matthias Eder, and Michaela Scherr. "Expression of the miR-17-92 polycistron in chronic myeloid leukemia (CML) CD34+ cells." Blood 109, no. 10 (February 6, 2007): 4399–405. http://dx.doi.org/10.1182/blood-2006-09-045104.

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Abstract Aberrant micro RNA (miRNA) expression has been described in human malignancies including B-cell lymphomas. We here report BCR-ABL– and c-MYC–dependent regulation of miRNA expression in chronic myeloid leukemia (CML) using microarray analysis (miCHIP) and miRNA-specific quantitative real-time reverse transcriptase–polymerase chain reaction (miR-qRT-PCR). In 3 bcr-abl–positive cell lines, expression of miRNAs encoded within the polycistronic miR-17-92 cluster is specifically down-regulated (2- to 5-fold) by both imatinib treatment and anti–BCR-ABL RNA interference (RNAi). In addition, anti–c-MYC RNAi reduces miR-17-92 expression in K562 cells in which miRNAs can specifically repress reporter gene expression, as demonstrated by specific miRNA inhibition with antagomirs. Furthermore, lentivirus-mediated overexpression of polycistronic miRNAs in K562 cells confers increased proliferation, partial resistance against anti–c-MYC RNAi, and enhanced sensitivity to imatinib-induced cell death. Finally, we determined miR-17-92 expression in purified normal (n = 4), early chronic-phase (CP) (n = 24), and blast-crisis (BC) (n = 7) CML CD34+ cells and found up-regulation of polycistronic pri-miRNA transcripts in CML and mature miRNAs in CP but not in BC CML. These data are in accordance with a BCR-ABL–c-MYC–miR-17-92 pathway that mediates enhanced miRNA expression in CP but not BC CML CD34+ cells. Altered miRNA expression may contribute to the pathophysiology of the disease and may provide potential targets for therapeutic intervention.

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Lu, Yongjun, Hui Zhou, Weixin Zhou, Yuanqi Zhu, and Lianghu Qu. "A novel snoRNA gene cluster in yeast is transcribed as polycistronic pre-snoRNAs." Science in China Series C: Life Sciences 42, no. 5 (October 1999): 529–37. http://dx.doi.org/10.1007/bf02881777.

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Daniels, Jan-Peter, Keith Gull, and Bill Wickstead. "Cell Biology of the Trypanosome Genome." Microbiology and Molecular Biology Reviews 74, no. 4 (December 2010): 552–69. http://dx.doi.org/10.1128/mmbr.00024-10.

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SUMMARY Trypanosomes are a group of protozoan eukaryotes, many of which are major parasites of humans and livestock. The genomes of trypanosomes and their modes of gene expression differ in several important aspects from those of other eukaryotic model organisms. Protein-coding genes are organized in large directional gene clusters on a genome-wide scale, and their polycistronic transcription is not generally regulated at initiation. Transcripts from these polycistrons are processed by global trans-splicing of pre-mRNA. Furthermore, in African trypanosomes, some protein-coding genes are transcribed by a multifunctional RNA polymerase I from a specialized extranucleolar compartment. The primary DNA sequence of the trypanosome genomes and their cellular organization have usually been treated as separate entities. However, it is becoming increasingly clear that in order to understand how a genome functions in a living cell, we will need to unravel how the one-dimensional genomic sequence and its trans-acting factors are arranged in the three-dimensional space of the eukaryotic nucleus. Understanding this cell biology of the genome will be crucial if we are to elucidate the genetic control mechanisms of parasitism. Here, we integrate the concepts of nuclear architecture, deduced largely from studies of yeast and mammalian nuclei, with recent developments in our knowledge of the trypanosome genome, gene expression, and nuclear organization. We also compare this nuclear organization to those in other systems in order to shed light on the evolution of nuclear architecture in eukaryotes.

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van Beilen, Jan B., Enrico G. Funhoff, Alexander van Loon, Andrea Just, Leo Kaysser, Manuel Bouza, René Holtackers, Martina Röthlisberger, Zhi Li, and Bernard Witholt. "Cytochrome P450 Alkane Hydroxylases of the CYP153 Family Are Common in Alkane-Degrading Eubacteria Lacking Integral Membrane Alkane Hydroxylases." Applied and Environmental Microbiology 72, no. 1 (January 2006): 59–65. http://dx.doi.org/10.1128/aem.72.1.59-65.2006.

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ABSTRACT Several strains that grow on medium-chain-length alkanes and catalyze interesting hydroxylation and epoxidation reactions do not possess integral membrane nonheme iron alkane hydroxylases. Using PCR, we show that most of these strains possess enzymes related to CYP153A1 and CYP153A6, cytochrome P450 enzymes that were characterized as alkane hydroxylases. A vector for the polycistronic coexpression of individual CYP153 genes with a ferredoxin gene and a ferredoxin reductase gene was constructed. Seven of the 11 CYP153 genes tested allowed Pseudomonas putida GPo12 recombinants to grow well on alkanes, providing evidence that the newly cloned P450s are indeed alkane hydroxylases.

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Journal articles on the topic 'Polycistronic gene'

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