A systematic nomenclature for mammalian tropomyosin isoforms

1Tropomyosin (Tpm) is a protein family associated with the stabilisation and regulation of the actin cytoskeleton (Gunning et al. ). It is expressed in opisthokonts including animals and fungi, but is not documented in plants, protists or procaryotes (Barua et al.; Cranz-Mileva et al. ). Tpm polymerises head to tail as a two-chained coiled coil along both sides of a helical actin filament stabilising the actin structure and interacting with a range of other actin binding proteins to regulate the actin cytoskeleton. The protein was discovered in the 1940s as a component of the actin filaments of striated muscle (Bailey ) and this remains the best studied example of Tpm function. In striated muscle, together with troponin, it enables calcium regulation of striated muscle contraction by blocking (−Ca2+) or allowing (+Ca2+) myosin access to its binding site on actin (Gordon et al.; Geeves ). Since the 1940s the different possible roles of Tpm and the number of interacting partners has multiplied (see special issue of J Muscle Res. Cell Motil., Marston & Gautel ). We now know that in mammalian cells Tpm is expressed from four separate genes and alternate promoter selection and splicing of each gene can produce up to 40 different mRNA variants most of which have been shown to be expressed as proteins in different tissues (Pittenger et al.; Vindin and Gunning ).

2The steady discovery of different splice variants in specific tissues has, over the years, led to a proliferation of different names for the isoforms, some identified with specific tissues but later found with a broader distribution. This has resulted in a great deal of confusion in the literature and it is often difficult, even for those of us in the field, to be sure which isoforms we are each referring to. It must be an even bigger nightmare for those trying to enter the field. The lack of a coherent nomenclature is an impediment to progress. We firmly believe that Tpm research is due for a renaissance from both the structure–function perspective in muscle research and the cytoplasmic perspective in the localisation-function of distinct isoforms and their binding partners. This is evidenced by the collection of articles published in a special issue of J Muscle Res Cell Motil devoted to Tpm Marston & Gautel. This renaissance will be enhanced if we can establish a widely agreed-upon nomenclature that the majority of active researchers will use. It will be much better if we can establish this now as the field begins to expand and other pressures develop on the nomenclature.

3After consulting colleagues working with Tpm we now make a specific proposal for how the nomenclature could be simplified and rationalised and to make it compatible with current best practice for gene and protein names. The proposal keeps as close as possible to some well-established historical precedents.

4Our suggestion is that any publication dealing with the tropomyosin protein should designate, at the first use, the formal name of the protein isoform as proposed here, and then define the short form or abbreviation that will be used thereafter in the article text. Reference to Tables 1, 2, 3 and 4 here will allow cross-reference to any earlier versions of the names used e.g., α-fast skeletal tropomyosin is Tpm1.1.

5The human tropomyosin genes should be known as TPM 1 through TPM 4 (Tpm 1 through Tpm 4 for mouse and rat tropomyosin) to be consistent with other gene nomenclatures.The protein short name Tm is historically well established but Tpm is consistent with standard protein nomenclature and is therefore preferred in the formal name.Tpm1 or Tpm2 specifies the protein is from gene TPM1 or TPM2 etc.Alternate isoforms are numbered systematically from one (e.g., Tpm1.1 etc.), keeping as close as possible to any precedent. Thus Tpm2.3 is the tropomyosin isoform from gene 2 isoform 3.In the formal name a subscript designates the tissue most closely associated, historically, with the protein isoform. Many such isoforms have been since found in multiple tissues and such designations are not always useful.St striated muscle, cardiac/skeletal tissueSm smooth muscle,Br brainCy other cytoplasmic The splicing of the four exons that vary in vertebrates can be designated by a four letter code; a.a.b.d indicates exon 1 is splice form a, exon 2 is splice form a, exon 6 is splice form b and exon 9 is splice form d.A dash as in b.-.b.d indicates that exon 2 is missing and therefore this is a short form of Tpm.Previous publications of Tpm isoforms have indicated that exon 9 can be a combination of two splice forms at the mRNA level (e.g., Vindin and Gunning ) but these reflect splice variants in non-coding regions at the 3′ end of the mRNA transcripts. We have therefore omitted such isoforms from our list of expressed proteins. The formal names of the two tropomyosins from the TPM 1 gene, found in the contractile filaments of smooth muscle, are thenTpm1.3Sm(a.a.b.d) and Tpm1.4Sm(a.a.a.d)

6The human tropomyosin genes should be known as TPM 1 through TPM 4 (Tpm 1 through Tpm 4 for mouse and rat tropomyosin) to be consistent with other gene nomenclatures.

7The protein short name Tm is historically well established but Tpm is consistent with standard protein nomenclature and is therefore preferred in the formal name.

8Tpm1 or Tpm2 specifies the protein is from gene TPM1 or TPM2 etc.

9Alternate isoforms are numbered systematically from one (e.g., Tpm1.1 etc.), keeping as close as possible to any precedent. Thus Tpm2.3 is the tropomyosin isoform from gene 2 isoform 3.

10In the formal name a subscript designates the tissue most closely associated, historically, with the protein isoform. Many such isoforms have been since found in multiple tissues and such designations are not always useful.St striated muscle, cardiac/skeletal tissueSm smooth muscle,Br brainCy other cytoplasmic

11St striated muscle, cardiac/skeletal tissue

12Sm smooth muscle,

13Br brain

14Cy other cytoplasmic

15The splicing of the four exons that vary in vertebrates can be designated by a four letter code; a.a.b.d indicates exon 1 is splice form a, exon 2 is splice form a, exon 6 is splice form b and exon 9 is splice form d.A dash as in b.-.b.d indicates that exon 2 is missing and therefore this is a short form of Tpm.Previous publications of Tpm isoforms have indicated that exon 9 can be a combination of two splice forms at the mRNA level (e.g., Vindin and Gunning ) but these reflect splice variants in non-coding regions at the 3′ end of the mRNA transcripts. We have therefore omitted such isoforms from our list of expressed proteins.

16A dash as in b.-.b.d indicates that exon 2 is missing and therefore this is a short form of Tpm.

17Previous publications of Tpm isoforms have indicated that exon 9 can be a combination of two splice forms at the mRNA level (e.g., Vindin and Gunning ) but these reflect splice variants in non-coding regions at the 3′ end of the mRNA transcripts. We have therefore omitted such isoforms from our list of expressed proteins.

18The formal names of the two tropomyosins from the TPM 1 gene, found in the contractile filaments of smooth muscle, are thenTpm1.3Sm(a.a.b.d) and Tpm1.4Sm(a.a.a.d)

19Tpm1.3Sm(a.a.b.d) and Tpm1.4Sm(a.a.a.d)

20The short form of the name would be Tpm1.3 and Tpm1.4

21Tables 1, 2, 3 and 4 list the current, known Tpm protein isoforms and the proposed formal names. As far as possible the alternate names for the same protein that have been used in the past are included in columns two and three. We also include, in Table 5, the full set of human Tpm amino acid sequences in the order that the exons appear in the gene. This will allow any ambiguity in the literature to be checked against the names and exon sequences used here. A fuller list of animal Tpm sequences can be found in Barua et al. and Schevzov et al..

22It is almost certain that additional isoforms of tropomyosin will be identified in these species. Consideration of all possible splicing combinations already established in at least one isoform leads to a calculation of 48 possible distinct isoforms in humans without consideration of currently unknown splicing alternatives. For example, Cooley and Bergtrom identified an increased number of potential isoforms from the TPM1 gene using RT-PCR. Our ability to detect and confirm additional isoforms will depend on both the extent of expression across, and the levels of expression in, different cell types.

23The NCBI accession numbers for each isoform are included in Tables 1, 2, 3 and 4 and the human, mouse and rat genes on the NCBI website have been amended to use the nomenclature as listed here.