Transcriptome sequencing of and microarray development for a Helicoverpa zea cell line to investigate in vitro insect cell-baculovirus interactions

PLoS ONE

Volumn 7, Issue 5, 2012, Pages

  Nguyen, Quan ^a   Palfreyman, Robin W ^a   Chan, Leslie C L ^a   Reid, Steven ^a   Nielsen, Lars K ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL; APOPTOSIS; ARTICLE; BACULOVIRUS; CARBON METABOLISM; CONTROLLED STUDY; DOWN REGULATION; GENE; HELICOVERPA ARMIGERA; HELICOVERPA ZEA; IMMUNE RESPONSE; INSECT; INSECT CELL; INSECT GENOME; MICROARRAY ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYHEDROSIS VIRUS; PROTEIN FUNCTION; RNA SEQUENCE; SEQUENCE ANALYSIS; SEQUENCE DATABASE; SEQUENCE HOMOLOGY; TRANSCRIPTOMICS; UPREGULATION; VIRUS CELL INTERACTION;

ANIMALS; BACULOVIRIDAE; CELL LINE; MICROARRAY ANALYSIS; MOLECULAR SEQUENCE DATA; MOTHS; SEQUENCE ANALYSIS, DNA; TRANSCRIPTOME; UP-REGULATION;

HELICOVERPA ZEA; HEXAPODA; MIRIDAE; NUCLEOPOLYHEDROVIRUS;

EID: 84862080240     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0036324     Document Type: Article

References (58)

1. Jacobson A, Foster R, Krupke C, Hutchison W, Pittendrigh B, et al. (2009) Resistance to Pyrethroid Insecticides in Helicoverpa zea (Lepidoptera: Noctuidae) in Indiana and Illinois. J Econ Entomol 102: 2289-2295.
2. Szewczyk B, Rabalski L, Krol E, Sihler W, de Souza ML, (2009) Baculovirus biopesticides- a safe alternative to chemical protection of plants. Journal of Biopesticides 2: 209-216.
3. Moscardi F, Souza ML, Castro MEB, Moscardi M, Szewczyk B, (2011) Baculovirus Pesticides: Present State and Future Perspectives. In: Ahmad I, Ahmad F, Pichtel J, editors. Microbes and Microbial Technology 1st ed. New York Springer pp. 415-445.
4. Kost TA, Condreay JP, Jarvis DL, (2005) Baculovirus as versatile vectors for protein expression in insect and mammalian cells. Nat Biotech 23: 567-575.
5. Mena JA, Kamen AA, (2011) Insect cell technology is a versatile and robust vaccine manufacturing platform. Expert Rev Vaccines 10: 1063-1081.
6. Chen CY, Lin CY, Chen GY, Hu YC, (2011) Baculovirus as a gene delivery vector: Recent understandings of molecular alterations in transduced cells and latest applications. Biotechnol Adv 29: 618-631.
7. Luo WY, Shih YS, Lo WH, Chen HR, Wang SC, et al. (2011) Baculovirus vectors for antiangiogenesis-based cancer gene therapy. Cancer Gene Ther 18: 637-645.
8. van Oers MM, Vlak JM, (2007) Baculovirus genomics. Curr Drug Targets 8: 1051-1068.
9. Xia Q, Zhou Z, Lu C, Cheng D, Dai F, et al. (2004) A Draft Sequence for the Genome of the domesticated silkworm (bombyx mori). Science 306: 1397.
10. The International Silkworm Genome Consortium, (2008) The genome of a lepidopteran model insect, the silkworm Bombyx mori. Insect Biochem Mol Biol 38: 1036-1045.
11. The International Aphid Genomics Consortium, (2010) Genome sequence of the Pea Aphid Acyrthosiphon pisum. PLoS Biol 8 doi:10.1371/journal.pbio.1000313.
12. Dong DJ, He HJ, Chai LQ, Jiang XJ, Wang JX, et al. (2007) Identification of genes differentially expressed during larval molting and metamorphosis of Helicoverpa armigera. BMC Dev Biol 7: 73.
13. Deng Y, Dong Y, Thodima V, Clem RJ, Passarelli AL, (2006) Analysis and functional annotation of expressed sequence tags from the fall armyworm Spodoptera frugiperda. BMC Genomics 7: 264.
14. Shelby KS, Popham HJR, (2009) Analysis of ESTs generated from immune-stimulated hemocytes of larval Heliothis virescens. J Invertebr Pathol 101: 86-95.
15. Pauchet Y, Wilkinson P, Munster MV, Augustin S, Pauron D, et al. (2009) Pyrosequencing of the midgut transcriptome of the poplar leaf beetle Chrysomela tremulae reveals new gene families in Coleoptera. Insect Biochem Mol Biol 39: 403-413.
16. Zagrobelny M, Scheibye AK, Jensen NB, Møller BL, Gorodkin J, et al. (2009) 454 pyrosequencing based transcriptome analysis of Zygaena filipendulae with focus on genes involved in biosynthesis of cyanogenic glucosides. BMC Genomics 10: 574.
17. Xia Z, Xu H, Zhai J, Li D, Luo H, et al. (2011) RNA-Seq analysis and de novo transcriptome assembly of Hevea brasiliensis. Plant Mol Biol 77: 299-308.
18. Vogel H, Altincicek B, Gloeckner G, Vilcinskas A, (2011) A comprehensive transcriptome and immune-gene repertoire of the lepidopteran model host Galleria mellonella. BMC Genomics 12: 308.
19. Oh S, Yoder-Himes DR, Tiedje J, Park J, Konstantinidis KT, (2010) Evaluating the performance of oligonucleotide microarrays for bacterial strains with increasing genetic divergence from the reference strain. Appl Environ Microbiol 76: 2980-2988.
20. Zerbino DR, Birney E, (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821-829.
21. Robertson G, Schein J, Chiu R, Corbett R, Field M, et al. (2010) De novo assembly and analysis of RNA-seq data. Nat Meth 7: 909-912.
22. Birol I, Jackman SD, Nielsen CB, Qian JQ, Varhol R, et al. (2009) De novo transcriptome assembly with ABySS. Bioinformatics 25: 2872-2877.
23. Wang XW, Luan JB, Li JM, Bao YY, Zhang CX, et al. (2010) Denovo characterization of a whitefly transcriptome and analysis of its gene expression during development. BMC Genomics 11: 400.
24. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29: 644-652.
25. Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM, (2010) The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res 38: 1767-1771.
26. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
27. Gotz S, Garcia GJM, Terol J, Williams TD, Nagaraj SH, et al. (2008) High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 36: 3420-3435.
28. Hu J, Bao J, Reecy JM, (2008) CateGOrizer: A web-based program to batch analyze gene ontology classification categories. Online J Bioinform 9: 108-112.
29. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M, (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35: 182-185.
30. Courtiade J, Pauchet Y, Vogel H, Heckel DG, (2011) A comprehensive characterization of the caspase gene family in insects from the order Lepidoptera. BMC Genomics 12: 357.
31. Zhang JY, Pan MH, Sun ZY, Huang SJ, Yu ZS, et al. (2010) The genomic underpinnings of apoptosis in the silkworm, Bombyx mori. BMC Genomics 11: 611.
32. Caspi R, Altman T, Dale JM, Dreher K, Fulcher CA, et al. (2010) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 38: 473-479.
33. Lyupina YV, Zatsepina OG, Timokhova AV, Orlova OV, Kostyuchenko MV, et al. (2011) New insights into the induction of the heat shock proteins in baculovirus infected insect cells. Virology 421: 34-41.
34. Sagisaka A, Fujita K, Nakamura Y, Ishibashi J, Noda H, et al. (2010) Genome-wide analysis of host gene expression in the silkworm cells infected with Bombyx mori nucleopolyhedrovirus. Virus Res 147: 166-175.
35. Bolstad BM, Irizarry RA, Astrand M, Speed TP, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193.
36. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, et al. (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102: 15545-15550.
37. Feldmeyer B, Wheat CW, Krezdorn N, Rotter B, Pfenninger M, (2011) Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance. BMC Genomics 12: 317.
38. Martin JA, Wang Z, (2011) Next-generation transcriptome assembly. Nat Rev Genet 12: 671-682.
39. Jacob NM, Kantardjieff A, Yusufi FNK, Retzel EF, Mulukutla BC, et al. (2010) Reaching the depth of the Chinese hamster ovary cell transcriptome. Biotechnol Bioeng 105: 1002-1009.
40. Toung JM, Morley M, Li M, Cheung VG, (2011) RNA-sequence analysis of human B-cells. Genome Res 21: 991-998.
41. Carinhas N, Bernal V, Monteiro F, Carrondo MJT, Oliveira R, et al. (2009) Improving baculovirus productional high celldensity through manipulation of energy metabolism. Metab Eng 12: 39-52.
42. MacDonald SJ, Thomas GH, Douglas AE, (2011) Genetic and metabolic determinants of nutritional phenotype in an insect-bacterial symbiosis. Mol Ecol 20: 2073-2084.
43. O'Riordan MXD, Bauler LD, Scott FL, Duckett CS, (2008) Inhibitor of apoptosis proteins in eukaryotic evolution and development: A model of thematic conservation. Dev Cell 15: 497-508.
44. Vandergaast R, Schultz KLW, Cerio RJ, Friesen PD, (2011) Active depletion of host cell inhibitor-of-apoptosis IAP triggers apoptosis upon Baculovirus DNA replication. J Virol 85 8348-8358.
45. Schultz KLW, Friesen PD, (2009) Baculovirus DNA replication-specific expression factors trigger apoptosis and shutoff of host protein synthesis during Infection. J Virol 83: 11123-11132.
46. Huang N, Wu W, Yang K, Passarelli AL, Rohrmann GF, et al. (2011) Baculovirus infection induces a DNA damage response that is required for efficient viral replication. J Virol 85 12547-11255.
47. Cory JS, Myers JH, (2003) The ecology and evolution of insect Baculoviruses. Annu Rev Ecol Evol Syst 34: 239-272.
48. Mcintosh AH, Ignoffo CM, (1983) Characterization of five cell lines established from species of Heliothis. Appl Entomol Zool 18: 262-269.
49. Nguyen Q, Qi YM, Wu Y, Chan LCL, Nielsen LK, et al. (2011) In vitro production of Helicoverpa baculovirus biopesticides- Automated selection of insect cell clones for manufacturing and systems biology studies. J Virol Methods 175: 197-205.
50. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
51. Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, et al. (2009) InterPro: the integrative protein signature database. Nucleic Acids Res 37: 211-215.
52. Karp PD, Suzanne MP, Markus K, Mario L, Joseph MD, et al. (2009) PathwayTools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief in bioinformatics 2: 40-79.
53. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M, (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 38: 355-360.
54. Smyth GK, (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3: Article3.
55. Benjamini Y, Hochberg Y, (1995) Controlling the False Discovery Rate- A Practical and Powerful Approach to Multiple Testing. J R Stat Soc Ser B Stat Methodol 57: 289-300.
56. Xue JL, Salem TZ, Turney CM, Cheng XW, (2010) Strategy of the use of 28S rRNA as a housekeeping gene in real-time quantitative PCR analysis of gene transcription in insect cells infected by viruses. J Virol Methods 163: 210-215.
57. Tanaka H, Ishibashi J, Fujita K, Nakajima Y, Sagisaka A, et al. (2008) A genome-wide analysis of genes and gene families involved in innate immunity of Bombyx mori. Insect Biochem Mol Biol 38: 1087-1110.
58. Vellozo AF, Veron AS, Baa PP, Huerta CJ, Cottret L, et al. (2011) CycADS: an annotation database system to ease the development and update of BioCyc databases. Database the journal of biological databases and curation 2011: bar008.