Molecular Analysis of a Family of Arabidopsis Genes Related to Galacturonosyltransferases
Yingzhen Kong, Gongke Zhou, Yanbin Yin, Ying Xu, Sivakumar Pattathil,
and Michael G. Hahn
Supplementary Data
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Kong et al. (2011) Supplemental Data
Table S1: Sources for the twelve genomes used for bioinformatic analysis of the GATL family.
Species / Abbr. / Clade / Genome Published in / Genome release versionPhyscomitrella patens ssp. patens / Pp / moss / (Rensing et al., 2008) / JGIv1.1
Selaginella moellendorffii / Sm / spike moss / Draft at / JGIv1.0
Oryza sativa / Os / monocot / (Goff et al., 2002; Yu et al., 2002) / TIGRv6.1
Sorghum bicolor / Sb / monocot / (Paterson et al., 2009) / JGIv1.0
Zea mays / Zm / monocot / (Schnable et al., 2009) / Maizesequence.org v4a.53
Brachypodium distachyon / Bd / monocot / (The International Brachypodium Initiative, 2010) / JGIv1.0
Vitis vinifera / Vv / dicot / (Jaillon et al., 2007) / Genoscope v1.0
Carica papaya / Cp / dicot / (Ming et al., 2008) / ftp://asgpb.mhpcc.hawaii.edu/papaya/
Arabidopsis thaliana / At / dicot / (The Arabidopsis Genome Initiative, 2000) / TAIRv9.0
Medicago truncatula / Mt / dicot / Draft at / Medicago.org v3.0
Glycine max / Gm / dicot / Draft at / JGIv1.0
Populus trichocarpa / Pt / dicot / (Tuskan et al., 2006); / JGIv2.0
Table S2: Summary of whole plant AtGATL expression patterns based on Figure 3.
Tissues in which AtGATL expression was observed are denoted with ●.
AtGATL1 / AtGATL2 / AtGATL3 / AtGATL4 / AtGATL5 / AtGATL6 / AtGATL7 / AtGATL8 / AtGATL9 / AtGATL10Cotyledon / ● / ● / ● / ● / ●
Primary leaves / ● / ● / ● / ● / ● / ● / ●
Shoot meristem / ● / ● / ● / ● / ● / ●
Root / ● / ● / ● / ● / ● / ● / ● / ● / ●
Root hair / ● / ●
Trichome / ● / ● / ● / ● / ● / ●
Stigma / ● / ● / ● / ●
Style / ●
Anther / ● / ● / ●
Filament / ● / ● / ●
Sepals / ● / ● / ● / ●
Petals / ● / ● / ●
Abscission zone / ● / ● / ● / ● / ●
Table S3: Summary of whole plant AtGATL expression patterns based on Figure 4.
Tissues in which AtGATL expression was observed are denoted with: for expression in upper stems; for expression in middle stems; for expression in lower stems; and for expression in hypocotyls. Note that AtGATL4 expression was only observed in pollen and pollen tubes in flowers.
AtGATL1 / AtGATL2 / AtGATL3 / AtGATL4 / AtGATL5 / AtGATL6 / AtGATL7 / AtGATL8 / AtGATL9 / AtGATL10Epidermis / / /
Cortex / / / /
Phloem / / / / /
Procambium /
Metaxylem / / /
Protoxylem / /
Secondary xylem / / / / / /
Pitch /
Fiber /
Interfascicular parenchyma /
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Kong et al. (2011) Supplemental Data
TableS4: Analysis of the topology of AtGATLs using the plant membrane protein database, Aramemnon.
The AtGATLs were queried for possible transmembrane spanning and N-terminal signal peptide domains using the Aramemnon database ( The GATL protein amino acid sequences were analyzed by 18 independent programs/models to reach a prediction of the protein topology. The results obtained are summarized in the table, which includes a statistic of how many of the programs in Aramemnon identified a hydrophobic N-terminal signal peptide domain for each GATL protein.
Protein / Soluble/Memb. Bound / Secretory Pathway / N terminal Hydrophobic Signal StatisticAtGATL1 / Soluble / +++ / 9/18
AtGATL2 / Soluble / +++ / 9/18
AtGATL3 / Soluble / +++ / 12/18
AtGATL4 / Soluble / +++ / 14/18
AtGATL5 / Soluble / +++ / 11/18
AtGATL6 / Soluble / +++ / 10/18
AtGATL7 / Soluble / +++ / 13/18
AtGATL8 / Soluble / +++ / 15/18
AtGATL9 / Soluble / +++ / 16/18
AtGATL10 / Soluble / ++ / 10/18
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Kong et al. (2011) Supplemental Data
Table S5: T-DNA insertion lines used in this study.
Locus / Gene name / SALK Line / Location of T-DNA insertion / Mutant Name / KO/KDAt1g13250 / AtGATL3 / SALK_114287 / 3’UTR / atgatl3 / KD
At1g02720 / AtGATL5 / SALK_106615 / exon / atgatl5 / KO
At4g02130 / AtGATL6 / SALK-032545 / 5’UTR / atgatl6 / KO
At1g24170 / AtGATL8 / SALK_049381 / exon / atgatl8 / KO
At1g70090 / AtGATL9 / SALK_091691 / exon / atgatl9 / KO
Table S6: Flanking primer sequences used for detection of insertions in AtGATL genes.
Locus / Gene name / Primer name / Primer sequenceAt1g13250 / AtGATL3 / 114287LP / 5’-CTGGAGAATCGATCTACGTCG-3’
114287RP / 5’-AGCCCAAAAGAATAATGTGGG-3’
At1g02720 / AtGATL5 / 106615LP / 5’-AACTCGAAATTGGCATCAATG-3’
106615RP / 5’-ATTCTCTGCTTTCTTCTCCGC-3’
At4g02130 / AtGATL6 / 032545LP / 5’-GAGAATGCATTAATATAGAATCGCC-3’
032545RP / 5’-TCTACGTCTAACGTGATCGCC-3’
At1g24170 / AtGATL8 / 049381-LP / 5’-CACAATGCTAAATCATTAGCCG-3’
049381-RP / 5’-TCATCAAGTCTAACCCATGGC-3’
At1g70090 / AtGATL9 / 091691-LP / 5’-AAGACAAGAAGAAACGGAGGC-3’
091691-RP / 5’-TGTCCTTCTTCTGCTTCATCTTC-3’
Table S7: Primers used for RT-PCR of AtGATL genes in tissue-specific expression studies.
Locus / Gene name / Primers name / Primer sequenceAt1g19300 / AtGATL1 / G1-F / 5’-TCAACGTCTCCTCCGTCTCT-3’
G1-R / 5’-TCCTAAACCGTGTTGGTTCC-3’
At3g50760 / AtGATL2 / G2-F / 5’-GCGCTAGACTCTCCGCTAAA-3’
G2-R / 5’-TGCAAATCTCGACACAGTCC-3’
At1g13250 / AtGATL3 / G3-F / 5’-TTTACCTCCGTGGCTCAGTC-3’
G3-R / 5’-TCCGAGATCAATCACCATCA-3’
At3g06260 / AtGATL4 / G4-F / 5’-AAACTACCTCCGTGGCACAA-3’
G4-R / 5’-ACAACCATCACCCCTGTGTT-3’
At1g02720 / AtGATL5 / G5-F / 5’-CCCCAACAAAACTCCGATTA-3’
G5-R / 5’-GAGCTCCGATTGTTCTCT G-3’
At4g02130 / AtGATL6 / G6-F / 5’-CTCTTTCCTCGTCTTCTTCTTC-3’
G6-R / 5’-GATTGAGCCACGCAGGTACT-3’
At3g62660 / AtGATL7 / G7-F / 5’-CGGAGGTGATAGAGAAATGGATG-3’
G7-R / 5’-CAACAAATCTGATTGTATCCTATGG-3’
At1g24170 / AtGATL8 / G8-F / 5’-GGATCATTACCACCGTTTCTTTTGG-3’
G8-R / 5’-AAGATTGAAACACAAGAGCGCCAG-3’
At1g70090 / AtGATL9 / G9-F / 5’-ATCATTACCACCGTTTCTTTTGGTG-3’
G9-R / 5’-GAAACACAAGAGCGCCAGAATGAC-3’
At3g28340 / AtGATL10 / G10-F / 5’-TGAAGAAACCACGGTCAAGA-3’
G10-R / 5’-GAGACCGTGTTGGTTCCATT-3’
At3g18780 / ACTIN / Act-1 / 5’-tggtCGTACAACCGGTATTGTGC-3’
Act-2 / 5’-TCATACGGTCAGCGATACCTGAG-3’
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Kong et al. (2011) Supplemental Data
Table S8: Primers used for construction of GATLpro::GUS fusions
Restriction sites are underlined and additional protection bps are added before each digestion site. For GATL3-3R and GATL43R primers, endogenous restriction sites within the 3’ region were used.
Locus / Gene name / Primer name / Primer sequenceAt1g19300 / AtGATL1 / GATL1-5F / 5’-TTTACTCTAGACAGAGAGTTCACACACACAGATGC-3’
GATL1-5R / 5’-TTTATCTAGAGGTTTCTTTCTTCTTCGTCGACTC-3’
GATL1-3R / 5’-AACTGAGCTCGACTACAAGACAAACAATAGAATGG-3’
GATL1-3F / 5’-AACTGAGCTC CCAGTCTCGATCGGTTTACTTATTAT-3’
At3g50760 / AtGATL2 / GATL2-5F / 5’-TTTACTCTAGATTGTTCACTGCACTGTGTCATGG-3’
GATL2-5R / 5’-ACCGAGGATCCATTTTTGTGCTAGAGAAACGTTAGATGCAAATG-3’
GATL2-3F / 5’-AACTGAGCTCATTTTAGATGTTAGTTTTCTTTTTTGGGGG-3’
GATL2-3R / 5’-AACTGAGCTCCTGTTTACCAAATTAGACATATCAAACCTAAG-3’
At1g13250 / AtGATL3 / GATL3-5F / 5’-TAATTCAAGCTTGTAAATGATAAGAAAACCATGTAGGC-3’
GATL3-5R / 5’-ACCGAGGATCCTTTTTTAGGTCTGTGTTGTGTAGTCTGTG-3’
GATL3-3F / 5’-AACTGAGCTCTTGTAACATCGGACGGTGGAGGAAG-3’
GATL3-3R / 5’-GTTTTCGTTTACGTGAGCTCAGAG-3’
At3g06260 / AtGATL4 / GATL4-5F / 5’-TAATTCAAGCTTGCTTTCTTTTCCTCGAGATAATTCCTTAC-3’
GATL4-5R / 5’-ACCGAGGATCCCCTGAACCTAATTCTCAGGTAAACTC-3’
GATL4-3F / 5’-AACTGAGGCCTAGAGGCAAAAGAAAAAAACCATTAAAC-3’
GATL4-3R / 5’-CGGTGTAAGCTTGTCGTCGGGAATTCC-3’
At1g02720 / AtGATL5 / GATL5-5F / 5’-TTTACTCTAGACAGTTTAGTTATTGCTCTCGTCTTTC-3’
GATL5-5R / 5’-AACGCTGGATCCTGCGAGGAATGCAGAAGAAACTAC-3’
GATL5-3F / 5’-AACTGAGCTCTGCCAATTTCGAGTTCGACATATTC-3’
GATL5-3R / 5’-AACTGAGCTCATGGTTCAAGTCTTGACGAGGATAG-3’
At4g02130 / AtGATL6 / GATL6-5F / 5’-TTTACTCTAGACATCCTCTTTGTGTTTTCACCCTGAAC-3’
GATL6-5R / 5’-ACCGAGGATCCTTCGAAAAAAGAACCAACGAAACCC-3’
GATL6-3F / 5’-AACTGAGCTCCGTTTCAGGTATAGAAAATTCTCAAAC-3’
GATL6-3R / 5’-AACTGAGCTCATTTGGATAATAGAGATTAGAGAGGAG-3’
At3g62660 / AtGATL7 / GATL7-5F / 5’-TCCCCCCGGGGAACATGTGTATAGTTGTCTTATACGAC-3’
GATL7-5R / 5’-TCCCCCCGGGCCTGAGAAATGAACCTCTGCGTTTC-3’
GATL7-3F / 5’-AACTGAGCTCTGATGATTGATGATCTCTGTTATTAC-3’
GATL7-3R / 5’-AACTGAGCTCTGAAACAGTGGCATATGTGTTATTTGG-3’
At1g24170 / AtGATL8 / GATL8-5F / 5’-TTACGCTGGATCCAAAGATCATCAGCTTCTTTGTCTCAAG-3’
GATL8-5R / 5’-AATTTCGGATCCTACTAAACAAAAACGCGTTTGAATGAATC-3’
GATL8-3F / 5’-AACTGAGCTCGAGTTTTAAAGTTACATTCTTTTTCAATATC-3’
GATL8-3R / 5’-AACTGAGCTCAAAAAAGAGAAGACTTGTCAAAAGAATAAC-3’
At1g70090 / AtGATL9 / GATL9-5F / 5’-CGCTGGATCCGAGGTTTATGTAGCTAAAGCCAAG-3’
GATL9-5R / 5’-AATTTCGGATCCTTTCAGAAAACGCGGTTTCTAAAGTGG-3’
GATL9-3F / 5’-AACTGAGCTCAGAGTTTGTGTAAGTCAACAACATTC-3’
GATL9-3R / 5’-AACTGAGCTCAATTACAGATTTGAGTGAGAGAGAG-3’
At3g28340 / AtGATL10 / GATL10-5F / 5’-CGCTGGATCCCACGTATGAATGTTTCTATTTCTCTAC-3’
GATL10-5R / 5’-ACGCTGGATCCCAAGAGAACTTAATGGCTAAGATC-3’
GATL10-3F / 5’-AACTGAGCTCTTTATTCATTTTTTGGGGTTTTGGTATGG-3’
GATL10-3R / 5’-AACTGAGCTCGCCTAAAAAAGTTTAAAATAGGGTTGAG-3’
Table S9: Primers used for construction of GATL::GFP fusions.
Restriction sites are underlined and additional protection bps are added before each digestion site.
Locus / Gene name / Primer name / Primer sequenceAt3g50760 / AtGATL2 / GATL2-S / 5’-AACTCATGACGATGACCTTAGACACAGC-3’
GATL2-AS / 5’-AATGGATCCACTCTCGATAAGGTCGAACCG-3’
At1g13250 / AtGATL3 / GATL3-S / 5’-AATTTCATGACGATGTCTTCTCTGCGTTTGCGTT-3’
GATL3-AS / 5’-AATTGGATCCGCTATCAGAGATCAACGGTGAATA-3’
At3g62660 / AtGATL7 / GATL7-S / 5’-AATCCATGGCGATGCTTTGGATCATGAG-3’
GATL-AS / 5’-AATTGGATCCGCGAGAGTAGTGTCCATAC-3’
At1g70090 / AtGATL9 / GATL9-S / 5’-AATATCATGACGATGCGGTTGCGTTTTCCG-3’
GATL9-AS / 5’-AATTGGATCCGAAAAAGCTTGAATCTTCTG-3’
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Kong et al. (2011) Supplemental Data
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