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Transcriptome analysis of cyst formation in Rhodospirillum centenum reveals large global changes in expression during cyst development.

Dong Q, Bauer CE - BMC Genomics (2015)

Bottom Line: Rhodospirillum centenum is a photosynthetic member of the Gram-negative Azospirillum clade members of which exhibit a complex developmental life-cycle featuring morphologically distinct cell types.Notable changes in expression occurred in numerous genes involved in cell wall and lipid biosynthesis, metabolic enzymes, and numerous regulatory genes such as histidine kinases and transcription factors.Many genes involved in protein synthesis and DNA replication were also significantly reduced during late stages of cyst development.

View Article: PubMed Central - PubMed

Affiliation: Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, 47405, USA. Dong3@indiana.edu.

ABSTRACT

Background: Rhodospirillum centenum is a photosynthetic member of the Gram-negative Azospirillum clade members of which exhibit a complex developmental life-cycle featuring morphologically distinct cell types. Under periods of nutrient deprivation, replicative vegetative cells differentiate into metabolically dormant cysts that survive harsh environmental stresses such as desiccation. Encystment involves a multi-stage developmental process that includes the rounding of cells, production of large intracellular storage granules of poly-hydroxybutyrate (PHB) and the excretion of a protective exopolysaccharide coating that envelops dormant cysts.

Results: To study the process of cyst development, we performed RNA-seq studies on cells that were induced to undergo cyst development. To assay for temporal changes in gene expression, RNA was extracted at 4, 24, 48, 72, 96 hours during development and subjected to deep sequence analysis. These results show that 812 genes exhibit log2 ≥ 1.5-fold changes in expression over a 96 hour cyst induction period demonstrating large global changes in gene expression during cyst development.

Conclusions: Notable changes in expression occurred in numerous genes involved in cell wall and lipid biosynthesis, metabolic enzymes, and numerous regulatory genes such as histidine kinases and transcription factors. Many genes involved in protein synthesis and DNA replication were also significantly reduced during late stages of cyst development. Genes previously identified by genetic screens as being critical for cyst development also exhibited changes of expression during cyst induction. This study provides the first transcriptome profile of global changes in gene expression that occur during development of cysts in a Gram-negative species.

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Time course expression profiles of representative carbon metabolism and energy production/storage genes (A), cell motility genes (B) and defense genes (C). Each column represents sample from one time-point. The maximum relative expression is green; the minimum is red.
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Fig6: Time course expression profiles of representative carbon metabolism and energy production/storage genes (A), cell motility genes (B) and defense genes (C). Each column represents sample from one time-point. The maximum relative expression is green; the minimum is red.

Mentions: One of the triggers for inducing cyst development is the growth on energy poor carbon sources such as the use of nutrient poor CENBA in this study [16,34]. Given that nutrient starvation is a signal for encystment it is interesting that there are no large alterations in carbon metabolism observed during cyst cell development. The few notable changes in expression include an operon coding for pyruvate dehydrogenase genes involved in the TCA cycle (pdhA, pdhB, pdhC and pdhD) that increased 6-fold in 72 hours and 96 hours of cyst development. We also found that a glyoxylate shunt pathway gene encoding isocitrate lyase aceA (RC1_2686) significantly decreased in middle and late stages of cyst developments. In addition, a gene coding for Tme that catalyzes the oxidative decarboxylation of malate to form pyruvate, is down-regulated 3-fold late in cyst development (Figure 6A).Figure 6


Transcriptome analysis of cyst formation in Rhodospirillum centenum reveals large global changes in expression during cyst development.

Dong Q, Bauer CE - BMC Genomics (2015)

Time course expression profiles of representative carbon metabolism and energy production/storage genes (A), cell motility genes (B) and defense genes (C). Each column represents sample from one time-point. The maximum relative expression is green; the minimum is red.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4340629&req=5

Fig6: Time course expression profiles of representative carbon metabolism and energy production/storage genes (A), cell motility genes (B) and defense genes (C). Each column represents sample from one time-point. The maximum relative expression is green; the minimum is red.
Mentions: One of the triggers for inducing cyst development is the growth on energy poor carbon sources such as the use of nutrient poor CENBA in this study [16,34]. Given that nutrient starvation is a signal for encystment it is interesting that there are no large alterations in carbon metabolism observed during cyst cell development. The few notable changes in expression include an operon coding for pyruvate dehydrogenase genes involved in the TCA cycle (pdhA, pdhB, pdhC and pdhD) that increased 6-fold in 72 hours and 96 hours of cyst development. We also found that a glyoxylate shunt pathway gene encoding isocitrate lyase aceA (RC1_2686) significantly decreased in middle and late stages of cyst developments. In addition, a gene coding for Tme that catalyzes the oxidative decarboxylation of malate to form pyruvate, is down-regulated 3-fold late in cyst development (Figure 6A).Figure 6

Bottom Line: Rhodospirillum centenum is a photosynthetic member of the Gram-negative Azospirillum clade members of which exhibit a complex developmental life-cycle featuring morphologically distinct cell types.Notable changes in expression occurred in numerous genes involved in cell wall and lipid biosynthesis, metabolic enzymes, and numerous regulatory genes such as histidine kinases and transcription factors.Many genes involved in protein synthesis and DNA replication were also significantly reduced during late stages of cyst development.

View Article: PubMed Central - PubMed

Affiliation: Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, 47405, USA. Dong3@indiana.edu.

ABSTRACT

Background: Rhodospirillum centenum is a photosynthetic member of the Gram-negative Azospirillum clade members of which exhibit a complex developmental life-cycle featuring morphologically distinct cell types. Under periods of nutrient deprivation, replicative vegetative cells differentiate into metabolically dormant cysts that survive harsh environmental stresses such as desiccation. Encystment involves a multi-stage developmental process that includes the rounding of cells, production of large intracellular storage granules of poly-hydroxybutyrate (PHB) and the excretion of a protective exopolysaccharide coating that envelops dormant cysts.

Results: To study the process of cyst development, we performed RNA-seq studies on cells that were induced to undergo cyst development. To assay for temporal changes in gene expression, RNA was extracted at 4, 24, 48, 72, 96 hours during development and subjected to deep sequence analysis. These results show that 812 genes exhibit log2 ≥ 1.5-fold changes in expression over a 96 hour cyst induction period demonstrating large global changes in gene expression during cyst development.

Conclusions: Notable changes in expression occurred in numerous genes involved in cell wall and lipid biosynthesis, metabolic enzymes, and numerous regulatory genes such as histidine kinases and transcription factors. Many genes involved in protein synthesis and DNA replication were also significantly reduced during late stages of cyst development. Genes previously identified by genetic screens as being critical for cyst development also exhibited changes of expression during cyst induction. This study provides the first transcriptome profile of global changes in gene expression that occur during development of cysts in a Gram-negative species.

Show MeSH
Related in: MedlinePlus