Article Figures & Data
Figures
- Fig. 1.
Phylogenetic comparison of the complete set of 35 different MIPs encoded in the Arabidopsis genome. Plant MIPs are divided into four distinct subfamilies: PIPs, TIPs, NIPs, and SIPs. Similar proteins within a subfamily, with a maximum of 30% divergence, are clustered in monophyletic groups. The first and the last digit in the protein name identify the group and the individual gene product, respectively. This tree was obtained using the whole alignment and the distance method. Omitting the none-conserved N- and C-terminal regions from the phylogenetic analysis does not break the defined groups; only the relative positions of PIP2;6 and TIP3s is changed. In this case PIP2;6 forms a separate branch between PIP2;4 and PIP2;5 and TIP3s branch between TIP2s andTIP4;1. The bar indicates the mean distance of 0.05 changes per amino acid residue.
- Fig. 2.
Bootstrap majority-rule consensus tree generated with the distance method. A bootstrap value of 100% indicates branches that were supported in all replicates of resampling of data. Branches with a bootstrap value of less than 50% are collapsed.
- Fig. 3.
Schematic structure of MIP encoding genes in Arabidopsis. Horizontal bars and gaps depict exons and intron positions, respectively. Parts encoding transmembrane helices H1 to H6 according to an alignment with GlpF are indicated by vertical bars. The color on the vertical bars shows homologous transmembrane helices in the first and second halves of the MIPs. The exons and transmembrane helices are drawn to scale but the positions of helices are schematic. Helices encoded on two exons are only indicated on the exon where the major part is encoded. Small indels in the alignment of different genes, positioned between two helices on the same exon, are not shown.
Tables
New Name1-a Johanson et al.1-b Weig et al.1-c AGI Gene1-d BAC Gene1-e Accession No.1-f Expressed Sequence Tag (EST)1-g Comments1-h PIP1;1 PIP1a PIP1a At3g61430 F2A19.30 CAB71073 Yes PIP1;2 PIP1b PIP1b At2g45960 F4I18.6 AAC28529 Yes AthH2, TMP-A PIP1;3 PIP1c PIP1c At1g01620 F22L4.16 AAF81320 Yes TMP-B PIP1;4 PIP1e TMP-C At4g00430 F5I10.2 AAF02782 Yes Exon 2 ends at 86,121, not 86,097; compare with TMP-C. PIP1;5 PIP1d pCR55 At4g23400 F16G20.100 CAA20461 Yes PIP2;1 PIP2a PIP2a At3g53420 F4P12_120 CAB67649 Yes PIP2;2 PIP2b PIP2b At2g37170 T2N18.7 AAD18142 Yes PIP2;3 PIP2c RD28 At2g37180 T2N18.6 AAD18141 Yes PIP2;4 PIP2f T04164 At5g60660 MUP24.8 BAB09839 Yes PIP2;5 PIP2d – At3g54820 F28P10.200 CAB41102 Yes PIP2;6 PIP2e T22419 At2g39010 T7F6.18 AAC79629 Yes PIP2;7 PIP3a PIP3 At4g35100 M4E13.150 CAA17774 Yes Salt-stress-inducible MIP PIP2;8 PIP3b – At2g16850 F12A24.3 AAC64216 Yes – Pseudo PIP3 – At2g16830 F12A24.1 AAC64228 ? Pseudogene encoding 26 amino acids with second NPA. Similar to F12A24.3. – – – – T8O111-i 77,410–77,455 ? Partial F5I10.2-like sequence encoding helix 4. – – – – F5I101-i 77,564–77,656 ? Partial F5I10.2-like sequence encoding loop B and helix 3. TIP1;1 γTIP1 γTIP At2g36830 T1J8.1 AAD31569 Yes TIP1;2 γTIP2 Z30833, T21060,T22237 At3g26520 MFE16.3 BAB01832 Yes Salt-stress-inducible TIP, γTIP2 TIP1;3 γTIP3 – At4g01470 F11O4.1 AAC62778 ? No introns TIP2;1 δTIP1 δTIP At3g16240 MYA6.5 BAB01264 Yes TIP2;2 δTIP2 Z18142 At4g17340 d14705w CAB10515 Yes TIP2;3 δTIP3 T20432,T76151 At5g47450 MNJ7.4 BAB09071 Yes TIP3;1 αTIP αTIP At1g73190 T18K17.14 AAG52132 Yes TIP3;2 βTIP βTIP At1g17810 F2H15.4 AAF97261 Yes TIP4;1 ɛTIP T21742 At2g25810 F17H15.16 AAC42249 Yes Similar to NtTIPa TIP5;1 ζTIP – At3g47440 T21L8.190 CAB51216 ? – Pseudo-γTIP2 – – F7P11-i 79,395–79,728 ? Pseudogene similar to MFE16.3, truncated, NPV instead of NPA, no exon 2. – Pseudo-δTIP – At1g52180 F9I5.3 AAF29403 ? Pseudogene, only exon 2, 124 amino acids. NIP1;1 NLM1 NLM1 At4g19030 F13C5.200 CAA16760 Yes Misannotated: delete amino acids 205 through 216; exon 4 starts at 86,879, not 86,915. NIP1;2 NLM2 NLM2 At4g18910 F13C5.80 CAA16748 Yes NIP2;1 NLM3 NLM4 At2g34390 T31E10.27 AAC26712 Yes1-j NIP3;1 NLM9 – At1g318801-k F5M6.28 AAG50717 ? F5M6.28 is missing exon 1; exon 1, 38,681 through 38,550; exon 2 starts at 38,310, long C terminus. NIP4;1 NLM4 – At5g37810 K22F20.9 BAB10360 ? NIP4;2 NLM5 NLM5 At5g37820 K22F20.10 BAB10361 Yes1-j NIP5;1 NLM6 NLM8 At4g10380 F24G24.180 CAB39791 Yes Long N terminus. NIP6;1 NLM7 NLM7 At1g80760 F23A5.11 AAF14664 Yes Long N terminus. NIP7;1 NLM8 NLM6 At3g06100 F28L1.3 AAF30303 Yes Intron 3, 8,151 through 7,945, avoids TT acceptor splice site, restores conserved length of exon 4. – Pseudo-NLM3 NLM3 At2g29870 T27A16.3 AAC35214 ? Pseudogene encoding 139 amino acids, missing first NPA. – Pseudo-NLM9 – At2g21020 F26H11.22 AAD29814 ? Pseudogene, version 3 missing second NPA. Alternate annotation results in two NPAs, but missing helix 3 and 4, long C terminus. SIP1;1 SIP1a – At3g04090 T6K12.29 AAF26804 Yes SIP1;2 SIP1b – At5g18290 MRG7.25 BAB09487 Yes SIP2;1 SIP2 – At3g56950 F24I3.30 CAB72165 Yes -
↵F1-a Proposed new names for Arabidopsis MIPs. When referring to the corresponding gene, the name is written in italics. Genes encoding partial MIP-like sequences without all transmembrane regions are regarded as nonfunctional pseudogenes. Pseudogenes are not included in the proposed nomenclature as indicated by “–”.
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↵F1-b Nomenclature used inJohansson et al. (2000) and in U. Johanson and S. Gustavsson (unpublished data).
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↵F1-c Nomenclature used in Weig et al. (1997) and Weig and Jakob (2000a, 2000b).
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↵F1-d Arabidopsis Genome Initiative (AGI) gene nomenclature; At3g56950 indicates gene no. 5,695 (counting from top) on chromosome 3.
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↵F1-e Gene name used in annotation of bacterial artificial chromosome (BAC) or P1 sequences.
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↵F1-f Protein accession no. for a translation of the corresponding gene. When a gene annotation is missing, the location in the BAC is given in base pairs.
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↵F1-g Matching EST found in databases. ?, Not found.
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↵F1-h Alternative exon/introns positions proposed and used in this paper and odd features of the gene or the encoded protein. Some older names found in the literature (Kaldenhoff et al., 1993; Shagan and Bar-Zvi, 1993; Shagan et al., 1993; Pih et al., 1999) and in Genbank accession no.AF057137.
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↵F1-i Not annotated.
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↵F1-j cDNA cloned by reverse transcriptase-PCR (Weig and Jakob, 2000b).
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↵F1-k At1g31880 has 285 amino acids added at the N terminus, previously annotated as a separate gene (F5M6.11). At1g31880 is missing 29 amino acids close to the C terminus.
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