Modeling-dependent protein characterization of the rice aldehyde dehydrogenase (ALDH) superfamily reveals distinct functional and structural features.

PloS One
Simeon O KotchoniManfredo J Seufferheld

Abstract

The completion of the rice genome sequence has made it possible to identify and characterize new genes and to perform comparative genomics studies across taxa. The aldehyde dehydrogenase (ALDH) gene superfamily encoding for NAD(P)(+)-dependent enzymes is found in all major plant and animal taxa. However, the characterization of plant ALDHs has lagged behind their animal- and prokaryotic-ALDH homologs. In plants, ALDHs are involved in abiotic stress tolerance, male sterility restoration, embryo development and seed viability and maturation. However, there is still no structural property-dependent functional characterization of ALDH protein superfamily in plants. In this paper, we identify members of the rice ALDH gene superfamily and use the evolutionary nesting events of retrotransposons and protein-modeling-based structural reconstitution to report the genetic and molecular and structural features of each member of the rice ALDH superfamily in abiotic/biotic stress responses and developmental processes. Our results indicate that rice-ALDHs are the most expanded plant ALDHs ever characterized. This work represents the first report of specific structural features mediating functionality of the whole families of ALDHs in an organ...Continue Reading

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Citations

Sep 7, 2014·Biotechnology Advances·Katerina ZelenaRalf G Berger
Dec 31, 2010·BMC Structural Biology·Jose C Jimenez-LopezSimeon O Kotchoni
Jan 5, 2011·PloS One·Simeon O KotchoniManfredo J Seufferheld
Jan 10, 2012·Gene·Simeon O KotchoniLamine Baba-Moussa
Feb 7, 2017·Bioscience, Biotechnology, and Biochemistry·Takayuki KondoMuneharu Esaka
Jan 30, 2013·The Journal of Toxicological Sciences·Komal Singh RasaputraNarayan C Rath
Feb 7, 2020·Proceedings of the National Academy of Sciences of the United States of America·Yinggen KeShiping Wang
Sep 29, 2011·Molecular Biology Reports·Emma W GachomoSimeon O Kotchoni

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Methods Mentioned

BETA
environmental stress
environmental stresses
Rice Genome Sequencing
transgenic

Software Mentioned

Swiss
TASSER
ME
PDBViewer
Adaptive Poisson - Boltzmann Solver ( APBS )
AMBER99
PyMOL
ANOLEA
PROCHECK
ExPASy

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