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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.

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Number of genes expressed in at least one time point during each of the three major stages of the T. thermophila life cycle.Expression is defined as signal intensity above 1× adjusted background (99 AUs), as described in the text. The number of genes expressed at each of the stages is shown beneath the identifier for each circle. Number of genes in composite categories discussed in the text (e.g., genes expressed during growth but not starvation) are indicated along the margins. A total of 21,178 genes are accounted for in the diagram. An additional 5,876 genes failed to show signal intensity >99 AUs at every time point and stage tested (discussed in the text). One gene had a value of exactly 99 AUs and consequently was excluded by the search criteria. The search conditions were those listed in Table S4.
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pone-0004429-g004: Number of genes expressed in at least one time point during each of the three major stages of the T. thermophila life cycle.Expression is defined as signal intensity above 1× adjusted background (99 AUs), as described in the text. The number of genes expressed at each of the stages is shown beneath the identifier for each circle. Number of genes in composite categories discussed in the text (e.g., genes expressed during growth but not starvation) are indicated along the margins. A total of 21,178 genes are accounted for in the diagram. An additional 5,876 genes failed to show signal intensity >99 AUs at every time point and stage tested (discussed in the text). One gene had a value of exactly 99 AUs and consequently was excluded by the search criteria. The search conditions were those listed in Table S4.

Mentions: Growth and starvation are commonly studied physiological states in Tetrahymena and starving cells also undergo a series of developmental changes that are prerequisites for conjugation to occur. During starvation, Tetrahymena cells also experience a morphological transformation in which they elongate and develop a long caudal cilium and swim rapidly [49], [50], presumably to facilitate dispersion as an adaptive strategy in seeking either a mate or richer environment. We sought to determine the extent of changes in gene expression that occur during these physiological/develolpmental states. Based on the earliest global studies of RNA hybridization in T. thermophila, it was argued that, of the total number of genes expressed in growing or starved cells, ∼80% were expressed in both conditions while ∼20% were specific to one of the two stages being compared [45]. Consistent with this proposal, the microarray analyses (Figure 4, Table S4) showed that ∼85% (16120) of the putative ORFs were expressed at both stages. Interestingly, greater than three times as many genes were expressed specifically during starvation (2227) as were expressed specifically during growth (678). Of the 2227 putative genes expressed in starvation, but not during growth, mRNAs from 1866 (84%) of them were also detectable during conjugation, and many (1118, nearly 50% of them) were present during the first three hours of starvation. It is important to emphasize that starvation initiates the first steps in the sexual stages of the life cycle of T. thermophila, during which cells change rapidly from vegetative cells unable to mate to mating-competent cells [12], [13], and that the sexual phase of the life cycle can proceed to completion in starved cells. These considerations likely account for many of the large number of mRNAs that are present in starved and early conjugating cells, but not in growing cells. Interestingly, a similar number of genes (2153, described below) are expressed specifically during conjugation.


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)

Number of genes expressed in at least one time point during each of the three major stages of the T. thermophila life cycle.Expression is defined as signal intensity above 1× adjusted background (99 AUs), as described in the text. The number of genes expressed at each of the stages is shown beneath the identifier for each circle. Number of genes in composite categories discussed in the text (e.g., genes expressed during growth but not starvation) are indicated along the margins. A total of 21,178 genes are accounted for in the diagram. An additional 5,876 genes failed to show signal intensity >99 AUs at every time point and stage tested (discussed in the text). One gene had a value of exactly 99 AUs and consequently was excluded by the search criteria. The search conditions were those listed in Table S4.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0004429-g004: Number of genes expressed in at least one time point during each of the three major stages of the T. thermophila life cycle.Expression is defined as signal intensity above 1× adjusted background (99 AUs), as described in the text. The number of genes expressed at each of the stages is shown beneath the identifier for each circle. Number of genes in composite categories discussed in the text (e.g., genes expressed during growth but not starvation) are indicated along the margins. A total of 21,178 genes are accounted for in the diagram. An additional 5,876 genes failed to show signal intensity >99 AUs at every time point and stage tested (discussed in the text). One gene had a value of exactly 99 AUs and consequently was excluded by the search criteria. The search conditions were those listed in Table S4.
Mentions: Growth and starvation are commonly studied physiological states in Tetrahymena and starving cells also undergo a series of developmental changes that are prerequisites for conjugation to occur. During starvation, Tetrahymena cells also experience a morphological transformation in which they elongate and develop a long caudal cilium and swim rapidly [49], [50], presumably to facilitate dispersion as an adaptive strategy in seeking either a mate or richer environment. We sought to determine the extent of changes in gene expression that occur during these physiological/develolpmental states. Based on the earliest global studies of RNA hybridization in T. thermophila, it was argued that, of the total number of genes expressed in growing or starved cells, ∼80% were expressed in both conditions while ∼20% were specific to one of the two stages being compared [45]. Consistent with this proposal, the microarray analyses (Figure 4, Table S4) showed that ∼85% (16120) of the putative ORFs were expressed at both stages. Interestingly, greater than three times as many genes were expressed specifically during starvation (2227) as were expressed specifically during growth (678). Of the 2227 putative genes expressed in starvation, but not during growth, mRNAs from 1866 (84%) of them were also detectable during conjugation, and many (1118, nearly 50% of them) were present during the first three hours of starvation. It is important to emphasize that starvation initiates the first steps in the sexual stages of the life cycle of T. thermophila, during which cells change rapidly from vegetative cells unable to mate to mating-competent cells [12], [13], and that the sexual phase of the life cycle can proceed to completion in starved cells. These considerations likely account for many of the large number of mRNAs that are present in starved and early conjugating cells, but not in growing cells. Interestingly, a similar number of genes (2153, described below) are expressed specifically during conjugation.

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