Limits...
Microarray analyses of gene expression during the Tetrahymena thermophila life cycle.

Miao W, Xiong J, Bowen J, Wang W, Liu Y, Braguinets O, Grigull J, Pearlman RE, Orias E, Gorovsky MA - PLoS ONE (2009)

Bottom Line: Strikingly, transcripts homologous to 1068 predicted genes are specifically expressed and 1753 are significantly up-regulated during conjugation.Genes encoding proteins known to interact or to function in complexes show similar expression patterns, indicating that co-ordinate expression with putative genes of known function can identify genes with related functions.New candidate genes associated with the RNAi-like process of DNA elimination and with meiosis are identified and the late stages of conjugation are shown to be characterized by specific expression of an unexpectedly large and diverse number of genes not involved in nuclear functions.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, University of Rochester, Rochester, New York, USA. miaowei530@yeah.net

ABSTRACT

Background: The model eukaryote, Tetrahymena thermophila, is the first ciliated protozoan whose genome has been sequenced, enabling genome-wide analysis of gene expression.

Methodology/principal findings: A genome-wide microarray platform containing the predicted coding sequences (putative genes) for T. thermophila is described, validated and used to study gene expression during the three major stages of the organism's life cycle: growth, starvation and conjugation.

Conclusions/significance: Of the approximately 27,000 predicted open reading frames, transcripts homologous to only approximately 5900 are not detectable in any of these life cycle stages, indicating that this single-celled organism does indeed contain a large number of functional genes. Transcripts from over 5000 predicted genes are expressed at levels >5x corrected background and 95 genes are expressed at >250x corrected background in all stages. Transcripts homologous to 91 predicted genes are specifically expressed and 155 more are highly up-regulated in growing cells, while 90 are specifically expressed and 616 are up-regulated during starvation. Strikingly, transcripts homologous to 1068 predicted genes are specifically expressed and 1753 are significantly up-regulated during conjugation. The patterns of gene expression during conjugation correlate well with the developmental stages of meiosis, nuclear differentiation and DNA elimination. The relationship between gene expression and chromosome fragmentation is analyzed. Genes encoding proteins known to interact or to function in complexes show similar expression patterns, indicating that co-ordinate expression with putative genes of known function can identify genes with related functions. New candidate genes associated with the RNAi-like process of DNA elimination and with meiosis are identified and the late stages of conjugation are shown to be characterized by specific expression of an unexpectedly large and diverse number of genes not involved in nuclear functions.

Show MeSH

Related in: MedlinePlus

Heat map of 217 codon biased genes described in reference [35].Clustering parameters, conditions and other symbols are as in Figure 6.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2636879&req=5

pone-0004429-g011: Heat map of 217 codon biased genes described in reference [35].Clustering parameters, conditions and other symbols are as in Figure 6.

Mentions: Analysis of the codon usage of predicted ORFs in the sequenced macronuclear genome [35] identified a subset of 232 genes that utilized a codon set that differed from that of the average gene. Marked codon biases are thought to be associated with mRNAs that are translated more rapidly or more accurately than average messages. These genes were represented in the EST database, on average, ∼15× more frequently than other genes, suggesting that a likely function of this codon bias is promoting more efficient translation of abundant proteins. Consistent with this suggestion, many of the genes in this subset encoded housekeeping proteins. Sixty-seven of these codon-biased genes lacked ESTs, leading Eisen et al. [35] to suggest they were either falsely predicted or might need to be transcribed rapidly and/or efficiently at some specific stage of the Tetrahymena life-cycle. As our microarray analyses covered a wide range of physiological/developmental stages and are subject to less bias than non-saturated, random analyses of cDNAs, we examined the expression of 217 of the 232 codon-biased genes that were included in the microarray design (Figure 11). Ninety-five percent of these genes (clusters b and c) showed high expression, especially the 146 genes (67.3%) in cluster c (Figure 11). Most were highly expressed during all stages. Only 3 genes in cluster a1 (TTHERM_00648580, TTHERM_00283180 and TTHERM_00654000; nomenclature as per http://www.ciliate.org) were not detectably transcribed at any of the stages examined; all 3 are likely to be wrongly predicted genes or wrongly designed probes (WM, unpublished observations). Thus, these codon-biased genes are mostly constitutively expressed, highly transcribed genes. Interestingly, of the 939 genes that are constitutively expressed at >50× corrected background, only 133 of them also show strong codon biases. A similar comparison of all genes constitutively expressed >100× corrected background indicates that only 99 of them (18.9%) also show codon biases. Thus, while most codon-biased genes are expressed constitutively and at high levels, not all highly expressed genes are codon-biased.


Microarray analyses of gene expression during the Tetrahymena thermophila life cycle.

Miao W, Xiong J, Bowen J, Wang W, Liu Y, Braguinets O, Grigull J, Pearlman RE, Orias E, Gorovsky MA - PLoS ONE (2009)

Heat map of 217 codon biased genes described in reference [35].Clustering parameters, conditions and other symbols are as in Figure 6.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2636879&req=5

pone-0004429-g011: Heat map of 217 codon biased genes described in reference [35].Clustering parameters, conditions and other symbols are as in Figure 6.
Mentions: Analysis of the codon usage of predicted ORFs in the sequenced macronuclear genome [35] identified a subset of 232 genes that utilized a codon set that differed from that of the average gene. Marked codon biases are thought to be associated with mRNAs that are translated more rapidly or more accurately than average messages. These genes were represented in the EST database, on average, ∼15× more frequently than other genes, suggesting that a likely function of this codon bias is promoting more efficient translation of abundant proteins. Consistent with this suggestion, many of the genes in this subset encoded housekeeping proteins. Sixty-seven of these codon-biased genes lacked ESTs, leading Eisen et al. [35] to suggest they were either falsely predicted or might need to be transcribed rapidly and/or efficiently at some specific stage of the Tetrahymena life-cycle. As our microarray analyses covered a wide range of physiological/developmental stages and are subject to less bias than non-saturated, random analyses of cDNAs, we examined the expression of 217 of the 232 codon-biased genes that were included in the microarray design (Figure 11). Ninety-five percent of these genes (clusters b and c) showed high expression, especially the 146 genes (67.3%) in cluster c (Figure 11). Most were highly expressed during all stages. Only 3 genes in cluster a1 (TTHERM_00648580, TTHERM_00283180 and TTHERM_00654000; nomenclature as per http://www.ciliate.org) were not detectably transcribed at any of the stages examined; all 3 are likely to be wrongly predicted genes or wrongly designed probes (WM, unpublished observations). Thus, these codon-biased genes are mostly constitutively expressed, highly transcribed genes. Interestingly, of the 939 genes that are constitutively expressed at >50× corrected background, only 133 of them also show strong codon biases. A similar comparison of all genes constitutively expressed >100× corrected background indicates that only 99 of them (18.9%) also show codon biases. Thus, while most codon-biased genes are expressed constitutively and at high levels, not all highly expressed genes are codon-biased.

Bottom Line: Strikingly, transcripts homologous to 1068 predicted genes are specifically expressed and 1753 are significantly up-regulated during conjugation.Genes encoding proteins known to interact or to function in complexes show similar expression patterns, indicating that co-ordinate expression with putative genes of known function can identify genes with related functions.New candidate genes associated with the RNAi-like process of DNA elimination and with meiosis are identified and the late stages of conjugation are shown to be characterized by specific expression of an unexpectedly large and diverse number of genes not involved in nuclear functions.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, University of Rochester, Rochester, New York, USA. miaowei530@yeah.net

ABSTRACT

Background: The model eukaryote, Tetrahymena thermophila, is the first ciliated protozoan whose genome has been sequenced, enabling genome-wide analysis of gene expression.

Methodology/principal findings: A genome-wide microarray platform containing the predicted coding sequences (putative genes) for T. thermophila is described, validated and used to study gene expression during the three major stages of the organism's life cycle: growth, starvation and conjugation.

Conclusions/significance: Of the approximately 27,000 predicted open reading frames, transcripts homologous to only approximately 5900 are not detectable in any of these life cycle stages, indicating that this single-celled organism does indeed contain a large number of functional genes. Transcripts from over 5000 predicted genes are expressed at levels >5x corrected background and 95 genes are expressed at >250x corrected background in all stages. Transcripts homologous to 91 predicted genes are specifically expressed and 155 more are highly up-regulated in growing cells, while 90 are specifically expressed and 616 are up-regulated during starvation. Strikingly, transcripts homologous to 1068 predicted genes are specifically expressed and 1753 are significantly up-regulated during conjugation. The patterns of gene expression during conjugation correlate well with the developmental stages of meiosis, nuclear differentiation and DNA elimination. The relationship between gene expression and chromosome fragmentation is analyzed. Genes encoding proteins known to interact or to function in complexes show similar expression patterns, indicating that co-ordinate expression with putative genes of known function can identify genes with related functions. New candidate genes associated with the RNAi-like process of DNA elimination and with meiosis are identified and the late stages of conjugation are shown to be characterized by specific expression of an unexpectedly large and diverse number of genes not involved in nuclear functions.

Show MeSH
Related in: MedlinePlus