Literature summary for 1.2.1.8 extracted from

Niu, X.; Zheng, W.; Lu, B.R.; Ren, G.; Huang, W.; Wang, S.; Liu, J.; Tang, Z.; Luo, D.; Wang, Y.; Liu, Y.
An unusual posttranscriptional processing in two betaine aldehyde dehydrogenase loci of cereal crops directed by short, direct repeats in response to stress conditions (2007), Plant Physiol., 143, 1929-1942.

Activating Compound

Activating Compound	Comment	Organism
NaCl	at a concentration of 0.1 M, expression of BADH1 is increased	Zea mays
NaCl	at a concentration of 0.1 M, expression of BADH2 is increased	Triticum aestivum
NaCl	at a concentration of 0.1 M, expression of BADH2 is increased	Zea mays
NaCl	expression of OsBADH1 gene was very low without salt stress and increased under salt stress conditions. However, a high ion concentration (0.5 M) inhibited trancription of this gene	Oryza sativa
NaCl	expression of OsBADH2 gene is low without salt stress and increased under salt stress conditions. A high ion concentration (0.5 M) inhibited trancription of the gene	Oryza sativa

Cloned(Commentary)

Cloned (Comment)	Organism
For OsBADH2, preliminary experiments based on RT-PCR show that the mRNA is expressed constitutively and multiple transcription products ae detected. Primers specific to the 5' region are used. To analyze the transcripts derived from the OsBADH2 gene, seedlings from different varieties under different rowth conditions are harvested for the total RNA isolation. As a result, all the 59 cDNA clones sequenced also have deletions at the 5' exonic region. Similar to that in the OsBADH1 gene, various unusual events in the OsBADH2 locus generate a number of truncated transcripts. The size of the deleted sequences from 5' UTR and exon(s) range from 112 to 523 nucleotides.	Oryza sativa
To compare the posttranscriptional processing patterns of the BADH homologs between cereal crop species and more distantly related dicotyledonous species, RT-PCR experiments using total RNA extracted from seedlings of spinach are conducted. Primers designed to amplify the full length of mRNA of BADH homologs are used. As anticipated, the RT-PCR products of BADH homologs from Arabidopsis are of expected size for correctly processed transcripts. Sequencing analysis of 4 cDNA clones confirms the correct processing.	Arabidopsis thaliana
To compare the posttranscriptional processing patterns of the BADH homologs between cereal crop species and more distantly related dicotyledonous species, RT-PCR experiments using total RNA extracted from seedlings of spinach are conducted. Primers designed to amplify the full length of mRNA of BADH homologs are used. As anticipated, the RT-PCR products of BADH homologs from spinach are of expected size for correctly processed transcripts. Sequencing analysis of 4 cDNA clones confirms the correct processing.	Spinacia oleracea
To compare the posttranscriptional processing patterns of the BADH homologs between cereal crop species and more distantly related dicotyledonous species, RT-PCR experiments using total RNA extracted from seedlings of spinach are conducted. Primers designed to amplify the full length of mRNA of BADH homologs are used. As anticipated, the RT-PCR products of BADH homologs from tomato are of expected size for correctly processed transcripts. Sequencing analysis of 3 cDNA clones confirms the correct processing.	Solanum lycopersicum
To determine whether the unusual events occurring in the BADH transcripts are specific only to the rice genome, RT-PCR experiments using the total RNA extracted from seedlings of maize species are carried out. These experiments used primers either to amplify the full length of mRNA or exclusively the 5' region of BADH homologs corresponding to those in rice. The sequencing data from a total of 6 cDNA clones demonstrate that all the tested cDNA clones have deletion(s) of the 5' exonic sequences resulting from the unusual posttranscriptional processing.	Zea mays
To determine whether the unusual events occurring in the transcripts are specific only to the rice genome, RT-PCR experiments using the total RNA extracted from seedlings of barley are performed. These experiments use primers either to amplify the full length of mRNA or exclusively the 5' region of BADH homologs corresponding to those in rice. The sequencing data from a total of 5 cDNA clones demonstrate that all the tested cDNA clones have deletions of the 5' exonic sequences resulting from the unusual posttranscriptional processing.	Hordeum vulgare
To determine whether the unusual events occurring in the transcripts are specific only to the rice genome, RT-PCR experiments using the total RNA extracted from seedlings of maize are performed. These experiments use primers either to amplify the full length of mRNA or exclusively the 5' region of BADH homologs corresponding to those in rice. The sequencing data from a total of 9 cDNA clones demonstrate that all the tested cDNA clones have deletions of the 5' exonic sequences resulting from the unusual posttranscriptional processing.	Zea mays
To determine whether the unusual events occurring in the transcripts are specific only to the rice genome, RT-PCR experiments using the total RNA extracted from seedlings of wheat are performed. These experiments use primers either to amplify the full length of mRNA or exclusively the 5' region of BADH homologs corresponding to those in rice. Sequencing data from 22 DNA clones demonstrate that all the tested cDNA clones had deletion(s) of the 5' exonic sequences resulting from the unusual posttranscriptional processing.	Triticum aestivum
To determine whether the unusual events occurring in the transcripts are specific only to the rice genome, RT-PCR experiments using the total RNA extracted from seedlings wheat are performed. These experiments use primers either to amplify the full length of mRNA or exclusively the 5' region of BADH homologs corresponding to those in rice. Sequencing data from 4 DNA clones demonstrate that all the tested cDNA clones had deletion(s) of the 5' exonic sequences resulting from the unusual posttranscriptional processing.	Triticum aestivum
To determine whether the unusual events occurring in the transcripts were specific only to the rice genome, RT-PCR experiments using the total RNA extracted from seedlings of barley are performed. These experiments use primers either to amplify the full length of mRNA or exclusively the 5' region of BADH homologs corresponding to those in rice. The sequencing data from a total of 6 cDNA clones demonstrate that all the tested cDNA clones have deletions of the 5' exonic sequences resulting from the unusual posttranscriptional processing.	Hordeum vulgare
to examine whether the expressed products are OsBADh1 gene, the RT-PCR-amplified fragments are cloned and sequenced. Primers derived from 5' and 3' untranslated regions are used to isolate the full length of OsBADH1 cDNA clones. Resultant sequencing analysis reveal that the cDNAs are truncated at the 5' exonic region. Observed expression products are shorter than the expected size of 695 bp of the 5' exonic region. Sequence comparison of the cDNAs reveal a considerable variation in their structural compositions. All of the cDNAs contain a deletion of the 5' coding sequence within the OsBADH1 gene. The deleted exon material ranged from 28 to 225 nucleotides in size. The start-point of the deletions in four cDNAs begin with the first nucleotide of the coding sequence, which give rise to the loss of translation initiation codon. 32 cDNAs encode derivatives with frame-shifts in the open reading frame , introducing various stop codons at different positions. Only 5 cDNA clones show the potential to encode partial BADH1 proteins with deletions that code for a part of the putative NAD+ binding domain. Most of the missing sequences from the truncated transcripts indicate above involved 2 different exons, and in a few cases the truncation take place within a single exon. In addition, two independent deletions of exon materials within a single cDNA clone are observed in 5 clones. Therefore, no cDNA is found to have the capacity to encode the full length of the OsBADH1 protein, indicating that correctly processed transcripts represent a very small proportion of the total cytoplasmic mature OsBADH1 RNA population and consequently that the majority of the OsBADH1 mRNAs are unlikely to encode functional proteins.	Oryza sativa

Inhibitors

Inhibitors	Comment	Organism
NaCl	In response to high salt stress conditions numerous truncated transcripts of two BADH homologs resulting from an unusual posttranscriptional processing are detected in barley. The observed events take place at the 5' exonic region, and lead to the insertion of exogenous gene sequences and a variety of deletions that result in the removal of translation initiation codon, loss of functional domain, and frameshifts with premature termination by introducing stop codon.; In response to high salt stress conditions numerous truncated transcripts of two BADH homologs resulting from an unusual posttranscriptional processing are detected in barley. The observed events take place at the 5' exonic region, and lead to the insertion of exogenous gene sequences and a variety of deletions that results in the removal of translation initiation codon, loss of functional domain, and frameshifts with premature termination by introducing stop codon.	Hordeum vulgare
NaCl	0.5 M, expression of OsBADH2 is increased under salt stress conditions, but at high concentrations, expression is inhibited.; 0.5 M, firstly, expression of OsBADH1 is increased under salt stress conditions, but at high concentrations, expression has been inhibited.	Oryza sativa
NaCl	at a concentration of 0.5 M, expression of BADH2 is inhibited	Triticum aestivum
NaCl	at a concentration of 0.5 M, expression of BADH1 is inhibited; at a concentration of 0.5 M, expression of BADH2 is inhibited	Zea mays

Localization

Localization	Comment	Organism	GeneOntology No.	Textmining
mitochondrion	-	Arabidopsis thaliana	5739	-

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.
betaine aldehyde + NAD+ + H2O	Solanum lycopersicum	-	glycine betaine + NADH + H+	-	?
betaine aldehyde + NAD+ + H2O	Spinacia oleracea	-	glycine betaine + NADH + H+	-	?
betaine aldehyde + NAD+ + H2O	Arabidopsis thaliana	-	glycine betaine + NADH + H+	-	?
betaine aldehyde + NAD+ + H2O	Hordeum vulgare	-	glycine betaine + NADH + H+	barley plants synthesize GB through catalytic reaction of the functional BADH protein, even though a large number of incorrectly processed BADH transcripts observed may considerably reduce the precise gene.	ir
betaine aldehyde + NAD+ + H2O	Hordeum vulgare	-	glycine betaine + NADH + H+	barley plants synthesize glycine betaine through catalytic reaction of the functional BADH protein, even though a large number of incorrectly processed BADH transcripts observe in this study may considerably reduce the precise gene	ir
betaine aldehyde + NAD+ + H2O	Oryza sativa	-	glycine betaine + NADH + H+	the appropriate level of glycine betaine may be regulated at both the transcriptional and posttranscriptional levels. Namely, the transcription is induced abundantly in response to the osmotic stresses, while the proper amount of precise gene products is balanced by posttranscriptional processing	ir
betaine aldehyde + NAD+ + H2O	Oryza sativa	-	glycine betaine + NADH + H+	the appropriate level of glycine may be regulated at both the transcriptional and posttranscriptional levels; namely, the transcription is induced abundantly in response to the osmotic stresses, while the proper amount of precise gene products is balanced by posttranscriptional processing	ir

Organism

Organism	UniProt	Comment	Textmining
Arabidopsis thaliana	Q9S795	-	-
Arabidopsis thaliana	Q9STS1	-	-
Hordeum vulgare	Q94IC0	-	-
Hordeum vulgare	Q94IC1	commentary	-
Oryza sativa	O24174	susp. japonica; susp. japonica and indica; different varieties are investigated	-
Oryza sativa	Q84LK3	subspecies japonica and indica	-
Solanum lycopersicum	-	-	-
Spinacia oleracea	P17202	-	-
Triticum aestivum	-	-	-
Triticum aestivum	Q8LGQ9	-	-
Zea mays	Q53CF4	-	-

Reaction

Reaction	Comment	Organism	Reaction ID
betaine aldehyde + NAD+ + H2O = betaine + NADH + 2 H+	the enzyme catalyzes the second step of the two-step conversion of choline into glycine betaine	Oryza sativa	a

Source Tissue

Source Tissue	Comment	Organism	Textmining
callus	source for isolating the total RNA	Oryza sativa	-
callus	source for isolating the totl RNA	Oryza sativa	-
leaf	mature leaf is used for isolating total RNA	Oryza sativa	-
leaf	mature leaf used for isolating the total RNA	Oryza sativa	-
seedling	source for isolating RNA	Triticum aestivum	-
seedling	source for isolating RNA	Solanum lycopersicum	-
seedling	source for isolating RNA	Zea mays	-
seedling	source for isolating RNA	Hordeum vulgare	-
seedling	source for isolating RNA	Spinacia oleracea	-
seedling	source for isolating RNA	Arabidopsis thaliana	-
seedling	source for isolating the total RNA	Oryza sativa	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
betaine aldehyde + NAD+ + H2O	-	Solanum lycopersicum	glycine betaine + NADH + H+	-	?
betaine aldehyde + NAD+ + H2O	-	Spinacia oleracea	glycine betaine + NADH + H+	-	?
betaine aldehyde + NAD+ + H2O	-	Arabidopsis thaliana	glycine betaine + NADH + H+	-	?
betaine aldehyde + NAD+ + H2O	-	Hordeum vulgare	glycine betaine + NADH + H+	barley plants synthesize GB through catalytic reaction of the functional BADH protein, even though a large number of incorrectly processed BADH transcripts observed may considerably reduce the precise gene.	ir
betaine aldehyde + NAD+ + H2O	-	Hordeum vulgare	glycine betaine + NADH + H+	barley plants synthesize glycine betaine through catalytic reaction of the functional BADH protein, even though a large number of incorrectly processed BADH transcripts observe in this study may considerably reduce the precise gene	ir
betaine aldehyde + NAD+ + H2O	-	Oryza sativa	glycine betaine + NADH + H+	the appropriate level of glycine betaine may be regulated at both the transcriptional and posttranscriptional levels. Namely, the transcription is induced abundantly in response to the osmotic stresses, while the proper amount of precise gene products is balanced by posttranscriptional processing	ir
betaine aldehyde + NAD+ + H2O	-	Oryza sativa	glycine betaine + NADH + H+	the appropriate level of glycine may be regulated at both the transcriptional and posttranscriptional levels; namely, the transcription is induced abundantly in response to the osmotic stresses, while the proper amount of precise gene products is balanced by posttranscriptional processing	ir

Subunits

Subunits	Comment	Organism
dimer	-	Oryza sativa

Synonyms

Synonyms	Comment	Organism
BADH	-	Triticum aestivum
BADH	-	Solanum lycopersicum
BADH	-	Oryza sativa
BADH	-	Zea mays
BADH	-	Hordeum vulgare
BADH	-	Spinacia oleracea
BADH	-	Arabidopsis thaliana
BADH1	-	Triticum aestivum
BADH1	-	Zea mays
BADH1	-	Hordeum vulgare
BADH1	-	Arabidopsis thaliana
BADH2	-	Zea mays
BADH2	-	Triticum aestivum
BADH2	-	Hordeum vulgare
BADH2	-	Arabidopsis thaliana
betaine aldehyde dehydrogenase	-	Triticum aestivum
betaine aldehyde dehydrogenase	-	Solanum lycopersicum
betaine aldehyde dehydrogenase	-	Oryza sativa
betaine aldehyde dehydrogenase	-	Zea mays
betaine aldehyde dehydrogenase	-	Hordeum vulgare
betaine aldehyde dehydrogenase	-	Spinacia oleracea
betaine aldehyde dehydrogenase	-	Arabidopsis thaliana
betaine aldehyde dehydrogenase 1, chloroplastic	-	Arabidopsis thaliana
betaine aldehyde dehydrogenase 2	-	Arabidopsis thaliana
betaine aldehyde dehydrogenase, chloroplastic	-	Spinacia oleracea
OsBADH1	-	Oryza sativa
OsBADH2	-	Oryza sativa