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In silico identification and characterization of N-Terminal acetyltransferase genes of poplar (Populus trichocarpa).

Zhu HY, Li CM, Wang LF, Bai H, Li YP, Yu WX, Xia DA, Liu CC - Int J Mol Sci (2014)

Bottom Line: N-terminal acetyltransferase (Nats) complex is responsible for protein N-terminal acetylation (Nα-acetylation), which is one of the most common covalent modifications of eukaryotic proteins.Although genome-wide investigation and characterization of Nat catalytic subunits (CS) and auxiliary subunits (AS) have been conducted in yeast and humans they remain unexplored in plants.Here we report on the identification of eleven genes encoding eleven putative Nat CS polypeptides, and five genes encoding five putative Nat AS polypeptides in Populus.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China. zhhy504@hotmail.com.

ABSTRACT
N-terminal acetyltransferase (Nats) complex is responsible for protein N-terminal acetylation (Nα-acetylation), which is one of the most common covalent modifications of eukaryotic proteins. Although genome-wide investigation and characterization of Nat catalytic subunits (CS) and auxiliary subunits (AS) have been conducted in yeast and humans they remain unexplored in plants. Here we report on the identification of eleven genes encoding eleven putative Nat CS polypeptides, and five genes encoding five putative Nat AS polypeptides in Populus. We document that the expansion of Nat CS genes occurs as duplicated blocks distributed across 10 of the 19 poplar chromosomes, likely only as a result of segmental duplication events. Based on phylogenetic analysis, poplar Nat CS were assigned to six subgroups, which corresponded well to the Nat CS types (CS of Nat A-F), being consistent with previous reports in humans and yeast. In silico analysis of microarray data showed that in the process of normal development of the poplar, their Nat CS and AS genes are commonly expressed at one relatively low level but share distinct tissue-specific expression patterns. This exhaustive survey of Nat genes in poplar provides important information to assist future studies on their functional role in poplar.

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Related in: MedlinePlus

Relative transcript abundance profiles of Populus Nat CS and AS genes across different tissues. A heat map displaying the transcript abundance is produced here using the genome-wide microarray data generated by Wilkins and coworkers [26]. The transcript abundance levels for the Populus Nat CS and AS genes were clustered using hierarchical clustering based on the Pearson correlation. The color scale at the bottom of each dendrogram represents log2 expression values, green color represents low level, red color represents high level of transcript abundances and black color represents no transcript expression. The symbols represent as follows: R, root; IN, internodes; N, nodes; YL, young leaf; ML, mature leaf.
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f4-ijms-15-01852: Relative transcript abundance profiles of Populus Nat CS and AS genes across different tissues. A heat map displaying the transcript abundance is produced here using the genome-wide microarray data generated by Wilkins and coworkers [26]. The transcript abundance levels for the Populus Nat CS and AS genes were clustered using hierarchical clustering based on the Pearson correlation. The color scale at the bottom of each dendrogram represents log2 expression values, green color represents low level, red color represents high level of transcript abundances and black color represents no transcript expression. The symbols represent as follows: R, root; IN, internodes; N, nodes; YL, young leaf; ML, mature leaf.

Mentions: Although numerous studies prior to this work were mainly focused on the expression, composition and function of Nats from several eukaryotes, such as yeast, mouse and human [24], such a systematic investigation had not yet been conducted in plants, especially for woody plants. Publicly available microarray data has often been considered as a reliable means of studying gene expression profiles [25]. To investigate the expression pattern of all poplar Nat CS and AS genes, the poplar Affymetrix microarray data [26] were reorganized in the Populus Genome Integrative Explorer (PopGenIE) [27]. All 16 poplar Nat genes including 11 CS and five AS genes have their corresponding transcript ID in the dataset and their expression profiles are displayed as shown Figure 4. It was found that expression of poplar Nat AS and CS genes in all five tissues were commonly low level in the process of normal development, but they also showed distinct tissue-specific expression patterns that were preferentially expressed in root (R), internode (IN), node (N) and young leaf (YL) while few in mature leaf (ML) (Figure 4). The highest expression level was found in the R, IN and YL, suggesting that in these tissues N-terminus of more proteins might be needed to undergo Nα-acetylation catalyzed by Nats for certain signal transmissions. The three genes encodingPtr Naa10p, Ptr Naa11p and Ptr Naa15p combined into Ptr NatA complex [28], have significantly similar expression patterns and high-level expression is mostly present in R and N (Figure 4). The expression profile of Ptr Naa20p, Ptr Naa21p and Ptr Naa25p genes encoding Ptr NatB complex showed also relatively consistently that transcript accumulation is focused on IN, few transcript expressions are focused on R, N, YL and ML. Furthermore, it was notable that consistent expression patterns were also found in the three genes encoding Ptr Naa30p, Ptr Naa31p and Ptr Naa35p combined into Ptr NatC complex, which have almost no expression in all five tissues. The evidence that poplar Nat CS and AS genes combined into the same Nat complex share similar expression patterns across tissues, seems likely to contribute to fast assembly from their individual subunit combination into active Nat complex.


In silico identification and characterization of N-Terminal acetyltransferase genes of poplar (Populus trichocarpa).

Zhu HY, Li CM, Wang LF, Bai H, Li YP, Yu WX, Xia DA, Liu CC - Int J Mol Sci (2014)

Relative transcript abundance profiles of Populus Nat CS and AS genes across different tissues. A heat map displaying the transcript abundance is produced here using the genome-wide microarray data generated by Wilkins and coworkers [26]. The transcript abundance levels for the Populus Nat CS and AS genes were clustered using hierarchical clustering based on the Pearson correlation. The color scale at the bottom of each dendrogram represents log2 expression values, green color represents low level, red color represents high level of transcript abundances and black color represents no transcript expression. The symbols represent as follows: R, root; IN, internodes; N, nodes; YL, young leaf; ML, mature leaf.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3958825&req=5

f4-ijms-15-01852: Relative transcript abundance profiles of Populus Nat CS and AS genes across different tissues. A heat map displaying the transcript abundance is produced here using the genome-wide microarray data generated by Wilkins and coworkers [26]. The transcript abundance levels for the Populus Nat CS and AS genes were clustered using hierarchical clustering based on the Pearson correlation. The color scale at the bottom of each dendrogram represents log2 expression values, green color represents low level, red color represents high level of transcript abundances and black color represents no transcript expression. The symbols represent as follows: R, root; IN, internodes; N, nodes; YL, young leaf; ML, mature leaf.
Mentions: Although numerous studies prior to this work were mainly focused on the expression, composition and function of Nats from several eukaryotes, such as yeast, mouse and human [24], such a systematic investigation had not yet been conducted in plants, especially for woody plants. Publicly available microarray data has often been considered as a reliable means of studying gene expression profiles [25]. To investigate the expression pattern of all poplar Nat CS and AS genes, the poplar Affymetrix microarray data [26] were reorganized in the Populus Genome Integrative Explorer (PopGenIE) [27]. All 16 poplar Nat genes including 11 CS and five AS genes have their corresponding transcript ID in the dataset and their expression profiles are displayed as shown Figure 4. It was found that expression of poplar Nat AS and CS genes in all five tissues were commonly low level in the process of normal development, but they also showed distinct tissue-specific expression patterns that were preferentially expressed in root (R), internode (IN), node (N) and young leaf (YL) while few in mature leaf (ML) (Figure 4). The highest expression level was found in the R, IN and YL, suggesting that in these tissues N-terminus of more proteins might be needed to undergo Nα-acetylation catalyzed by Nats for certain signal transmissions. The three genes encodingPtr Naa10p, Ptr Naa11p and Ptr Naa15p combined into Ptr NatA complex [28], have significantly similar expression patterns and high-level expression is mostly present in R and N (Figure 4). The expression profile of Ptr Naa20p, Ptr Naa21p and Ptr Naa25p genes encoding Ptr NatB complex showed also relatively consistently that transcript accumulation is focused on IN, few transcript expressions are focused on R, N, YL and ML. Furthermore, it was notable that consistent expression patterns were also found in the three genes encoding Ptr Naa30p, Ptr Naa31p and Ptr Naa35p combined into Ptr NatC complex, which have almost no expression in all five tissues. The evidence that poplar Nat CS and AS genes combined into the same Nat complex share similar expression patterns across tissues, seems likely to contribute to fast assembly from their individual subunit combination into active Nat complex.

Bottom Line: N-terminal acetyltransferase (Nats) complex is responsible for protein N-terminal acetylation (Nα-acetylation), which is one of the most common covalent modifications of eukaryotic proteins.Although genome-wide investigation and characterization of Nat catalytic subunits (CS) and auxiliary subunits (AS) have been conducted in yeast and humans they remain unexplored in plants.Here we report on the identification of eleven genes encoding eleven putative Nat CS polypeptides, and five genes encoding five putative Nat AS polypeptides in Populus.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China. zhhy504@hotmail.com.

ABSTRACT
N-terminal acetyltransferase (Nats) complex is responsible for protein N-terminal acetylation (Nα-acetylation), which is one of the most common covalent modifications of eukaryotic proteins. Although genome-wide investigation and characterization of Nat catalytic subunits (CS) and auxiliary subunits (AS) have been conducted in yeast and humans they remain unexplored in plants. Here we report on the identification of eleven genes encoding eleven putative Nat CS polypeptides, and five genes encoding five putative Nat AS polypeptides in Populus. We document that the expansion of Nat CS genes occurs as duplicated blocks distributed across 10 of the 19 poplar chromosomes, likely only as a result of segmental duplication events. Based on phylogenetic analysis, poplar Nat CS were assigned to six subgroups, which corresponded well to the Nat CS types (CS of Nat A-F), being consistent with previous reports in humans and yeast. In silico analysis of microarray data showed that in the process of normal development of the poplar, their Nat CS and AS genes are commonly expressed at one relatively low level but share distinct tissue-specific expression patterns. This exhaustive survey of Nat genes in poplar provides important information to assist future studies on their functional role in poplar.

Show MeSH
Related in: MedlinePlus