Characterization of the six zebrafish clade B fibrillar procollagen genes, with evidence for evolutionarily conserved alternative splicing within the pro-alpha1(V) C-propeptide

Matrix Biol. 2010 May;29(4):261-75. doi: 10.1016/j.matbio.2010.01.006. Epub 2010 Jan 25.


Genes for tetrapod fibrillar procollagen chains can be divided into two clades, A and B, based on sequence homologies and differences in protein domain and gene structures. Although the major fibrillar collagen types I-III comprise only clade A chains, the minor fibrillar collagen types V and XI comprise both clade A chains and the clade B chains pro-alpha1(V), pro-alpha3(V), pro-alpha1(XI) and pro-alpha2(XI), in which defects can underlie various genetic connective tissue disorders. Here we characterize the clade B procollagen chains of zebrafish. We demonstrate that in contrast to the four tetrapod clade B chains, zebrafish have six clade B chains, designated here as pro-alpha1(V), pro-alpha3(V)a and b, pro-alpha1(XI)a and b, and pro-alpha2(XI), based on synteny, sequence homologies, and features of protein domain and gene structures. Spatiotemporal expression patterns are described, as are conserved and non-conserved features that provide insights into the function and evolution of the clade B chain types. Such features include differential alternative splicing of NH(2)-terminal globular sequences and the first case of a non-triple helical imperfection in the COL1 domain of a clade B, or clade A, fibrillar procollagen chain. Evidence is also provided for previously unknown and evolutionarily conserved alternative splicing within the pro-alpha1(V) C-propeptide, which may affect selectivity of collagen type V/XI chain associations in species ranging from zebrafish to human. Data presented herein provide insights into the nature of clade B procollagen chains and should facilitate their study in the zebrafish model system.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Alternative Splicing*
  • Amino Acid Motifs / genetics
  • Animals
  • Base Sequence
  • Collagen Type III / genetics
  • Collagen Type III / metabolism
  • Collagen Type V / chemistry
  • Collagen Type V / genetics
  • Collagen Type V / metabolism*
  • Collagen* / chemistry
  • Collagen* / genetics
  • Collagen* / metabolism
  • Extracellular Matrix / genetics
  • Extracellular Matrix / metabolism
  • Genes
  • Humans
  • Procollagen / genetics*
  • Procollagen / metabolism
  • Protein Structure, Tertiary / genetics
  • Zebrafish / genetics
  • Zebrafish / metabolism


  • Collagen Type III
  • Collagen Type V
  • Procollagen
  • Collagen