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Genome-Wide Identification and Expression Analyses of Aquaporin Gene Family during Development and Abiotic Stress in Banana.

Hu W, Hou X, Huang C, Yan Y, Tie W, Ding Z, Wei Y, Liu J, Miao H, Lu Z, Li M, Xu B, Jin Z - Int J Mol Sci (2015)

Bottom Line: Expression analysis of MaAQP genes during fruit development and postharvest ripening showed that some MaAQP genes exhibited high expression levels during these stages, indicating the involvement of MaAQP genes in banana fruit development and ripening.Additionally, some MaAQP genes showed strong induction after stress treatment and therefore, may represent potential candidates for improving banana resistance to abiotic stress.Taken together, this study identified some excellent tissue-specific, fruit development- and ripening-dependent, and abiotic stress-responsive candidate MaAQP genes, which could lay a solid foundation for genetic improvement of banana cultivars.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, China. huwei2010916@126.com.

ABSTRACT
Aquaporins (AQPs) function to selectively control the flow of water and other small molecules through biological membranes, playing crucial roles in various biological processes. However, little information is available on the AQP gene family in bananas. In this study, we identified 47 banana AQP genes based on the banana genome sequence. Evolutionary analysis of AQPs from banana, Arabidopsis, poplar, and rice indicated that banana AQPs (MaAQPs) were clustered into four subfamilies. Conserved motif analysis showed that all banana AQPs contained the typical AQP-like or major intrinsic protein (MIP) domain. Gene structure analysis suggested the majority of MaAQPs had two to four introns with a highly specific number and length for each subfamily. Expression analysis of MaAQP genes during fruit development and postharvest ripening showed that some MaAQP genes exhibited high expression levels during these stages, indicating the involvement of MaAQP genes in banana fruit development and ripening. Additionally, some MaAQP genes showed strong induction after stress treatment and therefore, may represent potential candidates for improving banana resistance to abiotic stress. Taken together, this study identified some excellent tissue-specific, fruit development- and ripening-dependent, and abiotic stress-responsive candidate MaAQP genes, which could lay a solid foundation for genetic improvement of banana cultivars.

No MeSH data available.


Putative isoelectric point and relative molecular weight of plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), nodulin 26-like intrinsic proteins (NIPs) and small basic intrinsic proteins (SIPs) from banana and rice with ExPASy proteomics server database. MaPIP, MaTIP, MaNIP and MaSIP indicate AQPs from banana. OsPIP, OsTIP, OsNIP and OsSIP indicate AQPs from rice.
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ijms-16-19728-f001: Putative isoelectric point and relative molecular weight of plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), nodulin 26-like intrinsic proteins (NIPs) and small basic intrinsic proteins (SIPs) from banana and rice with ExPASy proteomics server database. MaPIP, MaTIP, MaNIP and MaSIP indicate AQPs from banana. OsPIP, OsTIP, OsNIP and OsSIP indicate AQPs from rice.

Mentions: To identify AQP family members from banana, a genome-wide search was carried out using both Hidden Markov Model and BLAST searches with 35 AQP genes from Arabidopsis and 34 AQP genes from rice as queries. A total of 47 non-redundant MaAQP genes were identified from the banana genome. All identified sequences of amino acids and full length cDNAs for banana AQPs were listed in Tables S1 and S2, respectively. Conserved domain and multiple sequence alignment analyses suggested that all identified banana AQPs contained the typical AQP family MIP domain. Prediction of transmembrane domains (TMDs) showed that most MaAQPs (26 of 47%, 55%) contained six TMDs, whereas the other 21 MaAQPs had 4, 5 or 7 predicted TMDs (Table S3). Further, we identified the NPA motifs and ar/R selectivity filter sequences of banana AQPs by multiple sequence alignment analysis with tomato AQPs as references (Table S4, Figures S1–S5) [28]. Both in the MaPIP and MaTIP subfamilies, the two NPA motifs are conserved with typical Asp-Pro-Ala residues. In the MaNIP subfamily, all the MaNIPs also show typical Asp-Pro-Ala residues, except for MaNIP3-2, where the alanine is replaced by a serine residue in the first NPA and by a valine in the second NPA. In the MaSIP subfamily, the first NPA have extensive variation, among which the alanine is replaced by threonine for MaSIP1-1 or by leucine for MaSIP2-1 and MaSIP2-2, whereas the second NPA are completely conserved. The ar/R filter showed an increased subfamily-specific sequence in comparison to the two NPA motifs. In the MaPIP subfamily, all MaPIPs showed an ar/R filter configuration typical for conserved residues in other species (F, H, T, R). In the MaTIP subfamily, the ar/R is formed by H/Q in H2, I/S/V/T in H5, A/G in LE1 and V/R in LE2. The MaNIP subfamily showed W/G/A in H2, V/S/I in H5, A/G in LE1 and R in LE2. In the MaSIP subfamily, the ar/R is constituted by L/Y/F in H2, T/K in H5, P/G in LE1 and N/S in LE2. To determine their protein characteristics, the isoelectric point (pI) and relative molecular mass (RMW) of banana AQP amino acid sequences were calculated using ExPASY (Table S5). The 47 predicted AQP proteins from banana ranged from 188 to 359 amino acid residues in length, with RMWs varying from 20.0 to 38.7 KDa. The protein characteristics of AQPs from banana and rice were compared according to their pI and RMW (Figure 1). In the PIP subfamily, the pI of most MaPIPs ranged from 9 to 10, and the RMW was approximately 20 kDa, whereas the pI of most OsPIPs ranged from 7 to 10 with a RMW of approximately 30 kDa. In the TIP subfamily, the pI of most TIPs was between 5 and 7 and the RMW was approximately 25 kDa both in banana and rice. In the NIP subfamily, the MaNIPs showed a broad RMW, whereas the OsNIPs displayed a wide range of pI. In the SIP subfamily, most SIPs from banana and rice showed similar RMW and pI. Generally, the protein characteristics of PIP and NIP subfamilies in banana were different from that in rice, implying their functional diversity.


Genome-Wide Identification and Expression Analyses of Aquaporin Gene Family during Development and Abiotic Stress in Banana.

Hu W, Hou X, Huang C, Yan Y, Tie W, Ding Z, Wei Y, Liu J, Miao H, Lu Z, Li M, Xu B, Jin Z - Int J Mol Sci (2015)

Putative isoelectric point and relative molecular weight of plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), nodulin 26-like intrinsic proteins (NIPs) and small basic intrinsic proteins (SIPs) from banana and rice with ExPASy proteomics server database. MaPIP, MaTIP, MaNIP and MaSIP indicate AQPs from banana. OsPIP, OsTIP, OsNIP and OsSIP indicate AQPs from rice.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4581322&req=5

ijms-16-19728-f001: Putative isoelectric point and relative molecular weight of plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), nodulin 26-like intrinsic proteins (NIPs) and small basic intrinsic proteins (SIPs) from banana and rice with ExPASy proteomics server database. MaPIP, MaTIP, MaNIP and MaSIP indicate AQPs from banana. OsPIP, OsTIP, OsNIP and OsSIP indicate AQPs from rice.
Mentions: To identify AQP family members from banana, a genome-wide search was carried out using both Hidden Markov Model and BLAST searches with 35 AQP genes from Arabidopsis and 34 AQP genes from rice as queries. A total of 47 non-redundant MaAQP genes were identified from the banana genome. All identified sequences of amino acids and full length cDNAs for banana AQPs were listed in Tables S1 and S2, respectively. Conserved domain and multiple sequence alignment analyses suggested that all identified banana AQPs contained the typical AQP family MIP domain. Prediction of transmembrane domains (TMDs) showed that most MaAQPs (26 of 47%, 55%) contained six TMDs, whereas the other 21 MaAQPs had 4, 5 or 7 predicted TMDs (Table S3). Further, we identified the NPA motifs and ar/R selectivity filter sequences of banana AQPs by multiple sequence alignment analysis with tomato AQPs as references (Table S4, Figures S1–S5) [28]. Both in the MaPIP and MaTIP subfamilies, the two NPA motifs are conserved with typical Asp-Pro-Ala residues. In the MaNIP subfamily, all the MaNIPs also show typical Asp-Pro-Ala residues, except for MaNIP3-2, where the alanine is replaced by a serine residue in the first NPA and by a valine in the second NPA. In the MaSIP subfamily, the first NPA have extensive variation, among which the alanine is replaced by threonine for MaSIP1-1 or by leucine for MaSIP2-1 and MaSIP2-2, whereas the second NPA are completely conserved. The ar/R filter showed an increased subfamily-specific sequence in comparison to the two NPA motifs. In the MaPIP subfamily, all MaPIPs showed an ar/R filter configuration typical for conserved residues in other species (F, H, T, R). In the MaTIP subfamily, the ar/R is formed by H/Q in H2, I/S/V/T in H5, A/G in LE1 and V/R in LE2. The MaNIP subfamily showed W/G/A in H2, V/S/I in H5, A/G in LE1 and R in LE2. In the MaSIP subfamily, the ar/R is constituted by L/Y/F in H2, T/K in H5, P/G in LE1 and N/S in LE2. To determine their protein characteristics, the isoelectric point (pI) and relative molecular mass (RMW) of banana AQP amino acid sequences were calculated using ExPASY (Table S5). The 47 predicted AQP proteins from banana ranged from 188 to 359 amino acid residues in length, with RMWs varying from 20.0 to 38.7 KDa. The protein characteristics of AQPs from banana and rice were compared according to their pI and RMW (Figure 1). In the PIP subfamily, the pI of most MaPIPs ranged from 9 to 10, and the RMW was approximately 20 kDa, whereas the pI of most OsPIPs ranged from 7 to 10 with a RMW of approximately 30 kDa. In the TIP subfamily, the pI of most TIPs was between 5 and 7 and the RMW was approximately 25 kDa both in banana and rice. In the NIP subfamily, the MaNIPs showed a broad RMW, whereas the OsNIPs displayed a wide range of pI. In the SIP subfamily, most SIPs from banana and rice showed similar RMW and pI. Generally, the protein characteristics of PIP and NIP subfamilies in banana were different from that in rice, implying their functional diversity.

Bottom Line: Expression analysis of MaAQP genes during fruit development and postharvest ripening showed that some MaAQP genes exhibited high expression levels during these stages, indicating the involvement of MaAQP genes in banana fruit development and ripening.Additionally, some MaAQP genes showed strong induction after stress treatment and therefore, may represent potential candidates for improving banana resistance to abiotic stress.Taken together, this study identified some excellent tissue-specific, fruit development- and ripening-dependent, and abiotic stress-responsive candidate MaAQP genes, which could lay a solid foundation for genetic improvement of banana cultivars.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, China. huwei2010916@126.com.

ABSTRACT
Aquaporins (AQPs) function to selectively control the flow of water and other small molecules through biological membranes, playing crucial roles in various biological processes. However, little information is available on the AQP gene family in bananas. In this study, we identified 47 banana AQP genes based on the banana genome sequence. Evolutionary analysis of AQPs from banana, Arabidopsis, poplar, and rice indicated that banana AQPs (MaAQPs) were clustered into four subfamilies. Conserved motif analysis showed that all banana AQPs contained the typical AQP-like or major intrinsic protein (MIP) domain. Gene structure analysis suggested the majority of MaAQPs had two to four introns with a highly specific number and length for each subfamily. Expression analysis of MaAQP genes during fruit development and postharvest ripening showed that some MaAQP genes exhibited high expression levels during these stages, indicating the involvement of MaAQP genes in banana fruit development and ripening. Additionally, some MaAQP genes showed strong induction after stress treatment and therefore, may represent potential candidates for improving banana resistance to abiotic stress. Taken together, this study identified some excellent tissue-specific, fruit development- and ripening-dependent, and abiotic stress-responsive candidate MaAQP genes, which could lay a solid foundation for genetic improvement of banana cultivars.

No MeSH data available.