The NTMC2 genes of embryophytes
From Purdue Genomics Database Facility
NTMC2 family members in currently available genomes
All of the nucleotide sequences described here, were obtained from http://www.ncbi.nlm.nih.gov or from http://genome.jgi-psf.org
NTMC2 family members in the Selaginella genome
NTMC2T1, NTMC2T2.1, NTMC2T2.2, NTMC2T2.3, NTMC2T3, NTMC2T5, NTMC2T6.1, NTMC2T6.2 plus a fragment of another NTMC2T6 gene.
Note that intron size is particularly small in Selaginella NTMC2 genes and comparatively large in Vitis NTMC2 genes.
NTMC2 family members in the Physcomitrella genome
NTMC2T1.1, NTMC2T1.2, NTMC2T1.3, NTMC2T2.1, NTMC2T2.2, NTMC2T2.3, NTMC2T3.1, NTMC2T3.2, NTMC2T4.1, NTMC2T4.2, NTMC2T4.3, NTMC2T5.1, NTMC2T5.2, NTMC2T5.3, NTMC2T6.1, NTMC2T6.2, NTMC2T6.3, NTMC2T6.4, NTMC2T6.5, NTMC2T6.6, plus a fragment of another NTMC2T6 gene.
NTMC2 family members in the Oryza genome
NTMC2T1.1, NTMC2T1.2, NTMC2T1.3, NTMC2T1.4, NTMC2T1.5, NTMC2T2.1, NTMC2T2.2, NTMC2T3, NTMC2T4.1, NTMC2T4.2, NTMC2T5, NTMC2T6.1, NTMC2T6.2
NTMC2 family members in the Sorghum genome
NTMC2T1.1, NTMC2T1.2, NTMC2T1.3, NTMC2T2.1, NTMC2T2.2, NTMC2T3, NTMC2T4.1, NTMC2T4.2, NTMC2T4.3, NTMC2T5, NTMC2T6.1, NTMC2T6.2
NTMC2 family members in the Arabidopsis genome
NTMC2T1.1, NTMC2T1.2, NTMC2T1.3, NTMC2T2.1, NTMC2T2.2, NTMC2T3, NTMC2T4, NTMC2T5.1, NTMC2T5.2, NTMC2T6.1, NTMC2T6.2 This describes the NTMC2 gene complement of both A.thaliana and A.lyrata. Sequences from each species are included in the list below.
NTMC2 family members in the Populus genome
NTMC2T1.1, NTMC2T1.2, NTMC2T1.3, NTMC2T1.4, NTMC2T2.1, NTMC2T2.2, NTMC2T2.3, NTMC2T3.1, NTMC2T3.2, NTMC2T4.1, NTMC2T4.2, NTMC2T5.1, NTMC2T5.2, NTMC2T6
NTMC2 family members in the Ricinus genome
NTMC2T1.1, NTMC2T1.2, NTMC2T1.3, NTMC2T1.4, NTMC2T2.1, NTMC2T2.2, NTMC2T3, NTMC2T4, NTMC2T5, NTMC2T6
NTMC2 family members in the Vitis genome
NTMC2T1.1, NTMC2T1.2, NTMC2T1.3, NTMC2T1.4, NTMC2T2.1, NTMC2T2.2, NTMC2T3.1, NTMC2T3.2, NTMC2T4, NTMC2T5, NTMC2T6
Family members
There are six plant NTMC2 gene families, Type 1 (NTMC2T1) to Type 6 (NTMC2T6). Each family comprises the members specific to a particular plant, of a homologous and evolutionarily conserved family of genes found in land plants. Each of the six plant gene families, has its own, conserved gene structure. Different plant species have different numbers of genes within individual NTMC2 families. All six families share amino acid sequence similarity and domain architecture similarity. In addition to the homology within each family, there is also homology between the NTMC2T1, NTMC2T2 and NTMC2T4 families. The NTMC2T1 and NTMC2T2 families are very similar to each other at the gene structure level, and appear to be related to the NTMC2T4 family by a gene fusion or fission event. Phylogenetic analysis of the currently available full-length plant gene products, indicates a closer relationship between NTMC2T2 and NTMC2T4 families, than between NTMC2T1 and NTMC2T4 families. Unlike Physcomitrella, which has three NTMC2T4 genes, Selaginella lacks NTMC2T4 genes. In common with Physcomitrella, Selaginella contains one NTMC2T2 family member which is truncated at the C-terminal end and which therefore lacks the second C2 domain. These truncated NTMC2T2 genes are intermediate between Type 2 and Type 4. The NTMC2T3 family is similar at a domain composition level, to the NTMC2T1 and NTMC2T2 families, and all three families are similar, at this level, to animal synaptotagmins. The NTMC2T3 family is not homologous to the NTMC2T1 and NTMC2T2 families. The NTMC2T3 family has its own, seperately conserved gene structure. While the NTMC2T5 and NTMC2T6 families appear unrelated to the other families at the gene structure level, a higher degree of amino acid sequence similarity exists between the NTMC2T3 and NTMC2T6 families.
Related genes
The amino acid sequence similarity and domain architecture similarity shared by the six plant NTMC2 gene families, is also shared by the FAM62 gene family, a homologous and evolutionarily conserved gene family found in metazoans. Amino acid sequence similarity and domain architecture similarity, as outlined above, is also shared by the Syt (synaptotagmin) gene family, another homologous and evolutionarily conserved gene family found in metazoans. The FAM62 gene family and Syt gene family are not homologous to each other, nor to any of the plant NTMC2 gene families. While there is a sizeable literature, dating back to 1990 [reference 1] on the functions of synaptotagmin genes (see also, a recent review [reference 2]) there is almost no literature concerning the possible functions of the FAM62 genes or the plant NTMC2 genes. One preliminary biochemical analysis of the human FAM62 proteins has been published [reference 3]. Plant synaptotagmin-like genes were first identified in the Arabidopsis genome in 2001 [reference 4]. On 16 December 2008, 2 papers dealing with the functional role of the Arabidopsis NTMC2T1.1 gene (referred to as SYT1) were published in Plant Cell [references 7 and 8]
Functional prediction
The domain architecture shared by all of these gene families implies integral membrane proteins, tethered by their N-terminal TM domain, which via their C2 domains, interact with lipids, other membranes and other proteins, sometimes in a calcium regulated manner. Some Syts lack a transmembrane sequence. Some Syt1 orthologues are known to encode synaptic vesicle proteins which act crucially in synaptic vesicle exocytosis. Please see [reference 5] for further details about all of this information. Note that the Physcomitrella NTMC2T1.2 gene has been identified as highly upregulated by ABA and drought-stress (see gene annotation details and [reference 6]). The Arabidopsis NTMC2T1.1 gene (SYT1) has now been identified as a required participant in the process of plasma membrane repair [references 7 and 8].
References
1. Perin MS, Fried VA, Mignery GA, Jahn R, Südhof TC. 1990, Nature 345 p260 - Phospholipid binding by a synaptic vesicle protein homologous to the regulatory region of protein kinase C.
2. Chapman ER. 2008, Annu Rev Biochem. - How Does Synaptotagmin Trigger Neurotransmitter Release?
3. Min SW, Chang WP, Südhof TC. 2007, Proc Natl Acad Sci U S A. 104 p3823 - E-Syts, a family of membranous Ca2+-sensor proteins with multiple C2 domains.
4. Craxton M. 2001, Genomics 77 p43 - Genomic analysis of synaptotagmin genes.
5. Craxton M. 2007, BMC Genomics 8:259 - Evolutionary genomics of plant genes encoding N-terminal-TM-C2 domain proteins and the similar FAM62 genes and synaptotagmin genes of metazoans. http://www.biomedcentral.com/1471-2164/8/259
6. Cuming AC, Cho SH, Kamisugi Y, Graham H, Quatrano RS. 2007, New Phytol. 176 p275 - Microarray analysis of transcriptional responses to abscisic acid and osmotic, salt, and drought stress in the moss, Physcomitrella patens.
7. Schapire A, Voigt B, Jasik J, Rosado A, Lopez-Cobollo R, Menzel D, Salinas J, Mancuso S, Valpuesta V, Baluska F, Botella M. Plant Cell 2008 - Arabidopsis Synaptotagmin 1 is required for the maintenance of plasma membrane integrity and cell viability. http://www.plantcell.org/cgi/doi/10.1105/tpc.108.063859
8. Yamazaki T, Kawamura Y, Minami A, Uemura M. Plant Cell 2008 - Calcium-dependent freezing tolerance in Arabidopsis involves membrane resealing via Synaptotagmin SYT1. http://www.plantcell.org/cgi/doi/10.1105/tpc.108.062679
