Limits...
Transcriptomic analysis of a moderately growing subisolate Botryococcus braunii 779 (Chlorophyta) in response to nitrogen deprivation.

Fang L, Sun D, Xu Z, He J, Qi S, Chen X, Chew W, Liu J - Biotechnol Biofuels (2015)

Bottom Line: We found that many homologous ESTs between A races 779 and Bot-88 are unknown sequences, implying that A race contains many unknown genes.Upon ND, reconfiguration of metabolisms for reducing power is apparent, suggesting that B. braunii 779 is rapidly adapting under ND condition by transcriptomic reprogramming.We propose that B. braunii transcriptomes provide a rich source for discovery of novel genes involved in hydrocarbon biosynthesis.

View Article: PubMed Central - PubMed

Affiliation: Collaborative Innovation Center of Deep Sea Biology, Ocean College, Zhejiang University, Hangzhou, 310058 Zhejiang China ; Dalian Ocean University, Dalian, 116023 Liaoning China.

ABSTRACT

Background: The colonial microalga Botryococcus braunii has been brought to people's attention for its conspicuous ability to accumulate a variety of lipids including hydrocarbons. B. braunii strains are classified into 3 races based on the types of hydrocarbons. A and B races are known to accumulate high level of lipids. However, their extreme slow growth rate has impeded its application for renewable biofuel production.

Results: In this study, we report the transcriptomic response of a moderately growing subisolate from the culture of Botryococcus sp. CCALA-779 upon nitrogen deprivation (ND). We show that the subisolate has an average growth rate of 0.52 g l(-1) day(-1) under photoautotrophic growth conditions and lipid content is enhanced to 75 % of CDW upon ND. Both rDNA sequence and hydrocarbon composition analyses indicate that the subisolate belongs to A race B. braunii. Hence, it is designated as B. braunii 779. We show that B. braunii 779 transcriptome shares homology to majority of the A race but not B race B. braunii ESTs, suggesting that transcriptomes of A race differ from that of B race. We found that many homologous ESTs between A races 779 and Bot-88 are unknown sequences, implying that A race contains many unknown genes. Pathway-based transcriptomic analysis indicates that energy metabolisms are among the top expressed functions in log-phase cells, indicating that the slow growth rate is a result that energy flow is directed to lipid biosynthesis but not population growth. Upon ND, reconfiguration of metabolisms for reducing power is apparent, suggesting that B. braunii 779 is rapidly adapting under ND condition by transcriptomic reprogramming.

Conclusions: Taken together, our result shows that the subisolate B. braunii 779, similar to the Gottingen strain, is useful for biofuel production. Difference between transcriptomes of A and B races implies that different races of B. braunii strains belong to different sub-species. Furthermore, there are many novel genes that are unique to A race, suggesting that sequences of many enzymes involved in hydrocarbon biosynthesis are not currently known. We propose that B. braunii transcriptomes provide a rich source for discovery of novel genes involved in hydrocarbon biosynthesis.

No MeSH data available.


Related in: MedlinePlus

Subsets of ESTs in a number of processes and pathways are most up-regulated and down-regulated upon ND in B. braunii 779 cells. a Distribution of ESTs associated with 4 GO functions and 6 KEGG pathways based on ranks by ratio. b Distribution of ESTs associated with unspecific dehydrogenase based on ranks by level (upper panel) and ratio (lower panel). The display is identical to Fig. 5. c Levels of chlorophyll content. The barplot shows the average level of chlorophyll contents in cells prior to (+N) and after (−N) ND. Error bar is derived from triplicates. d Efficiency of quantum yield of photosystem II. The bar plot shows the average level of efficiency of quantum yield (Y) of photosystem II in cells prior (+N) to and after (−N) ND.
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4552190&req=5

Fig6: Subsets of ESTs in a number of processes and pathways are most up-regulated and down-regulated upon ND in B. braunii 779 cells. a Distribution of ESTs associated with 4 GO functions and 6 KEGG pathways based on ranks by ratio. b Distribution of ESTs associated with unspecific dehydrogenase based on ranks by level (upper panel) and ratio (lower panel). The display is identical to Fig. 5. c Levels of chlorophyll content. The barplot shows the average level of chlorophyll contents in cells prior to (+N) and after (−N) ND. Error bar is derived from triplicates. d Efficiency of quantum yield of photosystem II. The bar plot shows the average level of efficiency of quantum yield (Y) of photosystem II in cells prior (+N) to and after (−N) ND.

Mentions: To investigate changes of transcriptional activities upon ND, levels of individual ESTs after ND were compared with those prior to ND. We assumed that if a subset of ESTs associated with a pathway was enriched within a window of 1024 ESTs ranked by ratio (i.e., fold change >2, p value <0.05 after Bonferroni correction), the subset of ESTs was potentially co-regulated by a common transcription regulatory network in response to ND. Using the sliding window approach along the sorted ESTs based on rank by ratio, we found that subsets of ESTs associated with 3 GO biological processes (i.e., carbohydrate metabolism, glycolysis, and photosynthesis) and 6 KEGG metabolic pathways (i.e., tyrosine metabolism, fluorene degradation, TCA cycle, glycolysis/gluconeogenesis, pentose phosphate pathway, carbon fixation) plus ribosome subunit were enriched in one of the 23 sliding windows (Fig. 6a).Fig. 6


Transcriptomic analysis of a moderately growing subisolate Botryococcus braunii 779 (Chlorophyta) in response to nitrogen deprivation.

Fang L, Sun D, Xu Z, He J, Qi S, Chen X, Chew W, Liu J - Biotechnol Biofuels (2015)

Subsets of ESTs in a number of processes and pathways are most up-regulated and down-regulated upon ND in B. braunii 779 cells. a Distribution of ESTs associated with 4 GO functions and 6 KEGG pathways based on ranks by ratio. b Distribution of ESTs associated with unspecific dehydrogenase based on ranks by level (upper panel) and ratio (lower panel). The display is identical to Fig. 5. c Levels of chlorophyll content. The barplot shows the average level of chlorophyll contents in cells prior to (+N) and after (−N) ND. Error bar is derived from triplicates. d Efficiency of quantum yield of photosystem II. The bar plot shows the average level of efficiency of quantum yield (Y) of photosystem II in cells prior (+N) to and after (−N) ND.
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4552190&req=5

Fig6: Subsets of ESTs in a number of processes and pathways are most up-regulated and down-regulated upon ND in B. braunii 779 cells. a Distribution of ESTs associated with 4 GO functions and 6 KEGG pathways based on ranks by ratio. b Distribution of ESTs associated with unspecific dehydrogenase based on ranks by level (upper panel) and ratio (lower panel). The display is identical to Fig. 5. c Levels of chlorophyll content. The barplot shows the average level of chlorophyll contents in cells prior to (+N) and after (−N) ND. Error bar is derived from triplicates. d Efficiency of quantum yield of photosystem II. The bar plot shows the average level of efficiency of quantum yield (Y) of photosystem II in cells prior (+N) to and after (−N) ND.
Mentions: To investigate changes of transcriptional activities upon ND, levels of individual ESTs after ND were compared with those prior to ND. We assumed that if a subset of ESTs associated with a pathway was enriched within a window of 1024 ESTs ranked by ratio (i.e., fold change >2, p value <0.05 after Bonferroni correction), the subset of ESTs was potentially co-regulated by a common transcription regulatory network in response to ND. Using the sliding window approach along the sorted ESTs based on rank by ratio, we found that subsets of ESTs associated with 3 GO biological processes (i.e., carbohydrate metabolism, glycolysis, and photosynthesis) and 6 KEGG metabolic pathways (i.e., tyrosine metabolism, fluorene degradation, TCA cycle, glycolysis/gluconeogenesis, pentose phosphate pathway, carbon fixation) plus ribosome subunit were enriched in one of the 23 sliding windows (Fig. 6a).Fig. 6

Bottom Line: We found that many homologous ESTs between A races 779 and Bot-88 are unknown sequences, implying that A race contains many unknown genes.Upon ND, reconfiguration of metabolisms for reducing power is apparent, suggesting that B. braunii 779 is rapidly adapting under ND condition by transcriptomic reprogramming.We propose that B. braunii transcriptomes provide a rich source for discovery of novel genes involved in hydrocarbon biosynthesis.

View Article: PubMed Central - PubMed

Affiliation: Collaborative Innovation Center of Deep Sea Biology, Ocean College, Zhejiang University, Hangzhou, 310058 Zhejiang China ; Dalian Ocean University, Dalian, 116023 Liaoning China.

ABSTRACT

Background: The colonial microalga Botryococcus braunii has been brought to people's attention for its conspicuous ability to accumulate a variety of lipids including hydrocarbons. B. braunii strains are classified into 3 races based on the types of hydrocarbons. A and B races are known to accumulate high level of lipids. However, their extreme slow growth rate has impeded its application for renewable biofuel production.

Results: In this study, we report the transcriptomic response of a moderately growing subisolate from the culture of Botryococcus sp. CCALA-779 upon nitrogen deprivation (ND). We show that the subisolate has an average growth rate of 0.52 g l(-1) day(-1) under photoautotrophic growth conditions and lipid content is enhanced to 75 % of CDW upon ND. Both rDNA sequence and hydrocarbon composition analyses indicate that the subisolate belongs to A race B. braunii. Hence, it is designated as B. braunii 779. We show that B. braunii 779 transcriptome shares homology to majority of the A race but not B race B. braunii ESTs, suggesting that transcriptomes of A race differ from that of B race. We found that many homologous ESTs between A races 779 and Bot-88 are unknown sequences, implying that A race contains many unknown genes. Pathway-based transcriptomic analysis indicates that energy metabolisms are among the top expressed functions in log-phase cells, indicating that the slow growth rate is a result that energy flow is directed to lipid biosynthesis but not population growth. Upon ND, reconfiguration of metabolisms for reducing power is apparent, suggesting that B. braunii 779 is rapidly adapting under ND condition by transcriptomic reprogramming.

Conclusions: Taken together, our result shows that the subisolate B. braunii 779, similar to the Gottingen strain, is useful for biofuel production. Difference between transcriptomes of A and B races implies that different races of B. braunii strains belong to different sub-species. Furthermore, there are many novel genes that are unique to A race, suggesting that sequences of many enzymes involved in hydrocarbon biosynthesis are not currently known. We propose that B. braunii transcriptomes provide a rich source for discovery of novel genes involved in hydrocarbon biosynthesis.

No MeSH data available.


Related in: MedlinePlus