Xylella fastidiosa gene expression analysis by DNA microarrays
Xylella fastidiosa genome sequencing has generated valuable data by identifying genes acting either on metabolic pathways or in associated pathogenicity and virulence. Based on available information on these genes, new strategies for studying their expression patterns, such as microarray technology,...
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| Published in | Genetics and molecular biology Vol. 32; no. 2; pp. 340 - 353 |
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| Main Authors | , , , , , |
| Format | Journal Article |
| Language | English |
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Brazil
Sociedade Brasileira de Genética
01.01.2009
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| Online Access | Get full text |
| ISSN | 1415-4757 1678-4685 1678-4685 |
| DOI | 10.1590/S1415-47572009005000038 |
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| Abstract | Xylella fastidiosa genome sequencing has generated valuable data by identifying genes acting either on metabolic pathways or in associated pathogenicity and virulence. Based on available information on these genes, new strategies for studying their expression patterns, such as microarray technology, were employed. A total of 2,600 primer pairs were synthesized and then used to generate fragments using the PCR technique. The arrays were hybridized against cDNAs labeled during reverse transcription reactions and which were obtained from bacteria grown under two different conditions (liquid XDM(2) and liquid BCYE). All data were statistically analyzed to verify which genes were differentially expressed. In addition to exploring conditions for X. fastidiosa genome-wide transcriptome analysis, the present work observed the differential expression of several classes of genes (energy, protein, amino acid and nucleotide metabolism, transport, degradation of substances, toxins and hypothetical proteins, among others). The understanding of expressed genes in these two different media will be useful in comprehending the metabolic characteristics of X. fastidiosa, and in evaluating how important certain genes are for the functioning and survival of these bacteria in plants. |
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| AbstractList | Xylella fastidiosa genome sequencing has generated valuable data by identifying genes acting either on metabolic pathways or in associated pathogenicity and virulence. Based on available information on these genes, new strategies for studying their expression patterns, such as microarray technology, were employed. A total of 2,600 primer pairs were synthesized and then used to generate fragments using the PCR technique. The arrays were hybridized against cDNAs labeled during reverse transcription reactions and which were obtained from bacteria grown under two different conditions (liquid XDM2 and liquid BCYE). All data were statistically analyzed to verify which genes were differentially expressed. In addition to exploring conditions for X. fastidiosa genome-wide transcriptome analysis, the present work observed the differential expression of several classes of genes (energy, protein, amino acid and nucleotide metabolism, transport, degradation of substances, toxins and hypothetical proteins, among others). The understanding of expressed genes in these two different media will be useful in comprehending the metabolic characteristics of X. fastidiosa, and in evaluating how important certain genes are for the functioning and survival of these bacteria in plants. Xylella fastidiosa genome sequencing has generated valuable data by identifying genes acting either on metabolic pathways or in associated pathogenicity and virulence. Based on available information on these genes, new strategies for studying their expression patterns, such as microarray technology, were employed. A total of 2,600 primer pairs were synthesized and then used to generate fragments using the PCR technique. The arrays were hybridized against cDNAs labeled during reverse transcription reactions and which were obtained from bacteria grown under two different conditions (liquid XDM(2) and liquid BCYE). All data were statistically analyzed to verify which genes were differentially expressed. In addition to exploring conditions for X. fastidiosa genome-wide transcriptome analysis, the present work observed the differential expression of several classes of genes (energy, protein, amino acid and nucleotide metabolism, transport, degradation of substances, toxins and hypothetical proteins, among others). The understanding of expressed genes in these two different media will be useful in comprehending the metabolic characteristics of X. fastidiosa, and in evaluating how important certain genes are for the functioning and survival of these bacteria in plants.Xylella fastidiosa genome sequencing has generated valuable data by identifying genes acting either on metabolic pathways or in associated pathogenicity and virulence. Based on available information on these genes, new strategies for studying their expression patterns, such as microarray technology, were employed. A total of 2,600 primer pairs were synthesized and then used to generate fragments using the PCR technique. The arrays were hybridized against cDNAs labeled during reverse transcription reactions and which were obtained from bacteria grown under two different conditions (liquid XDM(2) and liquid BCYE). All data were statistically analyzed to verify which genes were differentially expressed. In addition to exploring conditions for X. fastidiosa genome-wide transcriptome analysis, the present work observed the differential expression of several classes of genes (energy, protein, amino acid and nucleotide metabolism, transport, degradation of substances, toxins and hypothetical proteins, among others). The understanding of expressed genes in these two different media will be useful in comprehending the metabolic characteristics of X. fastidiosa, and in evaluating how important certain genes are for the functioning and survival of these bacteria in plants. Xylella fastidiosa genome sequencing has generated valuable data by identifying genes acting either on metabolic pathways or in associated pathogenicity and virulence. Based on available information on these genes, new strategies for studying their expression patterns, such as microarray technology, were employed. A total of 2,600 primer pairs were synthesized and then used to generate fragments using the PCR technique. The arrays were hybridized against cDNAs labeled during reverse transcription reactions and which were obtained from bacteria grown under two different conditions (liquid XDM(2) and liquid BCYE). All data were statistically analyzed to verify which genes were differentially expressed. In addition to exploring conditions for X. fastidiosa genome-wide transcriptome analysis, the present work observed the differential expression of several classes of genes (energy, protein, amino acid and nucleotide metabolism, transport, degradation of substances, toxins and hypothetical proteins, among others). The understanding of expressed genes in these two different media will be useful in comprehending the metabolic characteristics of X. fastidiosa, and in evaluating how important certain genes are for the functioning and survival of these bacteria in plants. Xylella fastidiosa genome sequencing has generated valuable data by identifying genes acting either on metabolic pathways or in associated pathogenicity and virulence. Based on available information on these genes, new strategies for studying their expression patterns, such as microarray technology, were employed. A total of 2,600 primer pairs were synthesized and then used to generate fragments using the PCR technique. The arrays were hybridized against cDNAs labeled during reverse transcription reactions and which were obtained from bacteria grown under two different conditions (liquid XDM 2 and liquid BCYE). All data were statistically analyzed to verify which genes were differentially expressed. In addition to exploring conditions for X. fastidiosa genome-wide transcriptome analysis, the present work observed the differential expression of several classes of genes (energy, protein, amino acid and nucleotide metabolism, transport, degradation of substances, toxins and hypothetical proteins, among others). The understanding of expressed genes in these two different media will be useful in comprehending the metabolic characteristics of X. fastidiosa, and in evaluating how important certain genes are for the functioning and survival of these bacteria in plants. |
| Author | Lemos, Eliana G.M. Travensolo, Regiane F. Costa, Maria V.C.G. Carareto-Alves, Lucia M. Lopes, Tiago J.S. Carrilho, Emanuel |
| AuthorAffiliation | 2 Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP Brazil 1 Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, Universidade Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, SP Brazil |
| AuthorAffiliation_xml | – name: 2 Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP Brazil – name: 1 Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, Universidade Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, SP Brazil – name: Universidade de São Paulo – name: Universidade Estadual Paulista |
| Author_xml | – sequence: 1 givenname: Regiane F. surname: Travensolo fullname: Travensolo, Regiane F. organization: Universidade Estadual Paulista ‘Júlio de Mesquita Filho’, Brazil; Universidade de São Paulo, Brazil – sequence: 2 givenname: Lucia M. surname: Carareto-Alves fullname: Carareto-Alves, Lucia M. organization: Universidade Estadual Paulista ‘Júlio de Mesquita Filho’, Brazil – sequence: 3 givenname: Maria V.C.G. surname: Costa fullname: Costa, Maria V.C.G. organization: Universidade Estadual Paulista ‘Júlio de Mesquita Filho’, Brazil – sequence: 4 givenname: Tiago J.S. surname: Lopes fullname: Lopes, Tiago J.S. organization: Universidade Estadual Paulista ‘Júlio de Mesquita Filho’, Brazil – sequence: 5 givenname: Emanuel surname: Carrilho fullname: Carrilho, Emanuel organization: Universidade de São Paulo, Brazil – sequence: 6 givenname: Eliana G.M. surname: Lemos fullname: Lemos, Eliana G.M. organization: Universidade Estadual Paulista ‘Júlio de Mesquita Filho’, Brazil |
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| Cites_doi | 10.1038/ng1032 10.1128/MMBR.66.2.272-299.2002 10.1016/S1369-5274(00)00121-1 10.1016/S0065-2504(08)60109-9 10.1016/S0966-842X(98)01318-3 10.1101/gr.6.7.639 10.1128/JB.180.6.1347-1353.1998 10.1146/annurev.biochem.69.1.183 10.1093/nar/gnf078 10.1007/s00284-002-3829-z 10.1016/S0378-1119(96)00829-3 10.1046/j.1365-2958.2000.01719.x 10.1073/pnas.091062498 10.1111/j.1574-6968.2001.tb10836.x 10.1128/JB.180.14.3556-3562.1998 10.1128/JB.181.20.6425-6440.1999 10.1016/S0092-8674(00)81149-6 10.1002/pmic.200390031 10.1128/JB.183.6.2117-2120.2001 10.1146/annurev.py.27.090189.001415 10.1590/S1415-47572003000200015 10.1074/jbc.M000800200 10.1038/35018003 10.1128/MMBR.63.1.161-173.1999 10.1128/jb.179.4.1280-1290.1997 10.1016/S0378-1097(02)01189-8 10.1016/S1387-2656(08)70056-5 10.1101/gr.930803 10.1093/bib/2.4.341 10.1094/MPMI-1-275 10.1007/s002030000218 10.1590/S0100-879X2002000600003 10.1093/emboj/17.13.3640 10.1016/0003-2697(87)90021-2 10.1128/AEM.42.2.357-363.1981 10.1046/j.1365-2958.1996.421953.x 10.1073/pnas.94.24.13057 10.1128/jb.174.8.2679-2687.1992 10.1016/0378-1119(91)90584-X |
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| SubjectTerms | BIOCHEMISTRY & MOLECULAR BIOLOGY DNA microarray gene expression GENETICS & HEREDITY Genetics of Microorganisms Xylella fastidiosa |
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| Title | Xylella fastidiosa gene expression analysis by DNA microarrays |
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