Tubulin polymerization promoting protein (TPPP) ortholog from Suberites domuncula and comparative analysis of TPPP/p25 gene family

AbstractSponges are one of the oldest metazoan phyla that are, due to their highly conservative nature, often referred to as the living fossils of multicellular animals. As such, they are a very important model for evolutionary, developmental and functional studies of Metazoa. Tubulin polymerization promoting proteins (TPPPs) are defined by the presence of p25-alpha domain (Pfam05517). Their functional characteristics resemble those of microtubule-associated proteins. Presence of TPPP homologous genes has been postulated in all eukaryotes with ciliated cells and their primary function has been proposed as some basic cilia-connected function. We present here the genomic structure and the corresponding cDNA sequence of one poriferan TPPP homolog (SdTPPP) isolated from the marine sponge Suberites domuncula; and a comparative analysis of TPPP homolog sequences and genomic structures from other Eukaryotes. Our results confirm the radiation of one TPPP homolog into three distinct genes in the Vertebrate lineage, but the origin of different sequences and their phylogenetic relationships show to be influenced by alternative protein isoforms, independent gene duplications, modularity of the p25-alpha domain and possible adaptational requirements to environmental conditions.

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Faculty Opinions recommendation of Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1026748.325361 ◽

2005 ◽

Author(s):

Arcady Mushegian

Keyword(s):

Subcellular Localization ◽

Pattern Classification ◽

Large Scale ◽

Protein Isoforms ◽

Scale Analysis ◽

Large Scale Analysis ◽

Alternative Protein

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Mammalian skeletal muscle C-protein: purification from bovine muscle, binding to titin and the characterization of a full-length human cDNA

Journal of Cell Science ◽

10.1242/jcs.102.4.769 ◽

1992 ◽

Vol 102 (4) ◽

pp. 769-778

Author(s):

D.O. Furst ◽

U. Vinkemeier ◽

K. Weber

Keyword(s):

Skeletal Muscle ◽

Protein Sequencing ◽

Protein Isoforms ◽

Fast Method ◽

Mammalian Skeletal Muscle ◽

Terminal Sequence ◽

C Protein ◽

Human Sequence ◽

Associated Proteins ◽

Bovine Skeletal Muscle

We report a fast method for the isolation of homogeneous C-protein from bovine skeletal muscle. In electron micrographs C-protein appears as short rods with a relatively uniform length of about 50 nm. Protein sequencing shows a single N-terminal sequence. Radio-labelled C-protein strongly decorates titin II and myosin rods but not myosin heads. Binding to titin II is retained in preparations lacking titin-associated proteins. Antibodies to bovine C-protein were used to screen a lambda gt11 cDNA library constructed from fetal human skeletal muscle. Clone HC38 is 3833 bp long and encodes a protein of 1138 amino acid residues. The start of the predicted sequence fits the N-terminal sequence of the bovine protein. All partial sequences obtained from the bovine protein (348 residues) and the sequence deduced from a partial chicken cDNA (Einheber and Fischman, 1990) can be aligned along the human sequence. The sequences of human and chicken C-proteins share 50% identity and 70% similarity. Along the repeat patterns of the human protein the fibronectin (Fn)-like domains are better conserved than the immunoglobulin (Ig)-like domains. Regions of strong divergence between chicken fast C-protein and human slow C-protein may represent differences in C-protein isoforms.

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Proteins from morphologically differentiated neuroblastoma cells promote tubulin polymerization.

The Journal of Cell Biology ◽

10.1083/jcb.76.2.547 ◽

1978 ◽

Vol 76 (2) ◽

pp. 547-555 ◽

Cited By ~ 24

Author(s):

N W Seeds ◽

R B Maccioni

Keyword(s):

High Speed ◽

Gradient Centrifugation ◽

Neuroblastoma Cells ◽

Morphological Differentiation ◽

Tubulin Polymerization ◽

Associated Proteins ◽

Neurite Formation ◽

Brain Microtubules ◽

Brain Tubulin

Clonal cells (N18) of the mouse neuroblastoma C-1300 can be induced to undergo a morphological differentiation characterized by the outgrowth of very long neurites (> 150 microns) that contain many microtubules. Because the marked increase in the number and length of microtubules is apparently not due to an increase in the concentration of tubulin subunits, the possible role of additional macromolecules in the regulation of tubulin polymerization during neurite formation by N18 cells was examined. Using an in vitro system where the polymerization of low concentrations (< 4 mg/ml) of purified brain tubulin requires microtubule-associated proteins (MAPs), high-speed supernates (250,000 g) from neuroblastoma and glioma cells were assayed for their ability to replace MAPs in the polymerization of brain tubulin. Only the supernates from "differentiated" N18 cells were polymerization competent. Electron microscope observations of these supernates failed to demonstrate the presence of nucleation structures (rings or disks). The active factor(s) sedimented at approximately 7S on sucrose gradient centrifugation and eluted from 4B Sepharose in the region of 170,000 mol wt proteins. Furthermore, the inactive supernates from other cells did not inhibit polymerization when tested in the presence of limiting MAPs. Thus, microtubule formation accompanying neurite outgrowth in neuroblastoma cells appears to be regulated by the presence of additional macromolecular factor(s) that may be functionally equivalent to the MAPs found with brain microtubules.

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The structure of SAV1646 fromStaphylococcus aureusbelonging to a new `ribosome-associated' subfamily of bacterial proteins

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s1399004714025619 ◽

2015 ◽

Vol 71 (2) ◽

pp. 332-337 ◽

Cited By ~ 2

Author(s):

Yuri N. Chirgadze ◽

Teresa E. Clarke ◽

Vladimir Romanov ◽

Gera Kisselman ◽

Jean Wu-Brown ◽

...

Keyword(s):

Ribosomal Proteins ◽

Rotation Axis ◽

Genomic Structure ◽

Large Subunit ◽

Functional Model ◽

Homology Search ◽

Bacterial Proteins ◽

Bacterial Ribosome ◽

Acid Protein ◽

Associated Proteins

The crystal structure of the SAV1646 protein from the pathogenic microorganismStaphylococcus aureushas been determined at 1.7 Å resolution. The 106-amino-acid protein forms a two-layer sandwich with α/β topology. The protein molecules associate as dimers in the crystal and in solution, with the monomers related by a pseudo-twofold rotation axis. A sequence-homology search identified the protein as a member of a new subfamily of yet uncharacterized bacterial `ribosome-associated' proteins with at least 13 members to date. A detailed analysis of the crystal protein structure along with the genomic structure of the operon containing thesav1646gene allowed a tentative functional model of this protein to be proposed. The SAV1646 dimer is assumed to form a complex with ribosomal proteins L21 and L27 which could help to complete the assembly of the large subunit of the ribosome.

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Alternatively spliced isoforms reveal a novel type of PTB domain in CCM2 protein

Scientific Reports ◽

10.1038/s41598-019-52386-0 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 5

Author(s):

Xiaoting Jiang ◽

Akhil Padarti ◽

Yanchun Qu ◽

Shen Sheng ◽

Johnathan Abou-Fadel ◽

...

Keyword(s):

Genomic Structure ◽

Expression Patterns ◽

Genetic Mutation ◽

Protein Isoforms ◽

Start Codon ◽

Transcriptional Level ◽

Alternative Promoters ◽

Cavernous Malformations ◽

Cellular Expression ◽

Ptb Domain

Abstract Cerebral cavernous malformations (CCMs) is a microvascular disorder in the central nervous system. Despite tremendous efforts, the causal genetic mutation in some CCM patients has not be identified, raising the possibility of an unknown CCM locus. The CCM2/MGC4607 gene has been identified as one of three known genes causing CCMs. In this report, we defined a total of 29 novel exons and 4 novel promoters in CCM2 genomic structure and subsequently identified a total of 50 new alternative spliced isoforms of CCM2 which eventually generated 22 novel protein isoforms. Genetic analysis of CCM2 isoforms revealed that the CCM2 isoforms can be classified into two groups based on their alternative promoters and alternative start codon exons. Our data demonstrated that CCM2 isoforms not only are specific in their subcellular compartmentation but also have distinct cellular expression patterns among various tissues and cells, indicating the pleiotropic cellular roles of CCM2 through their multiple isoforms. In fact, the complexity of the CCM2 genomic structure was reflected by the multiple layers of regulation of CCM2 expression patterns. At the transcriptional level, it is accomplished by alternative promoters, alternative splicing, and multiple transcriptional start sites and termination sites; while at the translational level, it is carried out with various cellular functions with a distinguishable CCM2 protein group pattern, specified abundance and composition of selective isoforms in a cell and tissue specific fashion. Through experimentation, we discovered a unique phosphotyrosine binding (PTB) domain, namely atypical phosphotyrosine binding (aPTB) domain. Some long CCM2 isoform proteins contain both classes of PTB domains, making them a dual PTB domain-containing protein. Both CCM1 and CCM3 can bind competitively to this aPTB domain, indicating CCM2 as the cornerstone for CCM signaling complex (CSC).

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Netrin Family: Role for Protein Isoforms in Cancer

Journal of Nucleic Acids ◽

10.1155/2019/3947123 ◽

2019 ◽

Vol 2019 ◽

pp. 1-9 ◽

Cited By ~ 4

Author(s):

Caroline Suzanne Bruikman ◽

Huayu Zhang ◽

Anneli Maite Kemper ◽

Janine Maria van Gils

Keyword(s):

Cell Migration ◽

Alternative Splicing ◽

Special Interest ◽

Tumor Biology ◽

Family Members ◽

Axonal Guidance ◽

Protein Isoforms ◽

Family Role ◽

Associated Proteins

Netrins form a family of secreted and membrane-associated proteins. Netrins are involved in processes for axonal guidance, morphogenesis, and angiogenesis by regulating cell migration and survival. These processes are of special interest in tumor biology. From the netrin genes various isoforms are translated and regulated by alternative splicing. We review here the diversity of isoforms of the netrin family members and their known and potential roles in cancer.

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Full-length transcriptome reconstruction reveals a large diversity of RNA and protein isoforms in rat hippocampus

Nature Communications ◽

10.1038/s41467-019-13037-0 ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 6

Author(s):

Xi Wang ◽

Xintian You ◽

Julian D. Langer ◽

Jingyi Hou ◽

Fiona Rupprecht ◽

...

Keyword(s):

Gene Annotation ◽

Full Length ◽

Protein Isoforms ◽

Rat Hippocampus ◽

Reading Frame ◽

Functional Studies ◽

Third Generation Sequencing ◽

Isoform Diversity ◽

Polysome Profiling ◽

Ribosome Footprinting

Abstract Gene annotation is a critical resource in genomics research. Many computational approaches have been developed to assemble transcriptomes based on high-throughput short-read sequencing, however, only with limited accuracy. Here, we combine next-generation and third-generation sequencing to reconstruct a full-length transcriptome in the rat hippocampus, which is further validated using independent 5´ and 3´-end profiling approaches. In total, we detect 28,268 full-length transcripts (FLTs), covering 6,380 RefSeq genes and 849 unannotated loci. Based on these FLTs, we discover co-occurring alternative RNA processing events. Integrating with polysome profiling and ribosome footprinting data, we predict isoform-specific translational status and reconstruct an open reading frame (ORF)-eome. Notably, a high proportion of the predicted ORFs are validated by mass spectrometry-based proteomics. Moreover, we identify isoforms with subcellular localization pattern in neurons. Collectively, our data advance our knowledge of RNA and protein isoform diversity in the rat brain and provide a rich resource for functional studies.

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Influence of Intron Length on Alternative Splicing of CD44

Molecular and Cellular Biology ◽

10.1128/mcb.18.10.5930 ◽

1998 ◽

Vol 18 (10) ◽

pp. 5930-5941 ◽

Cited By ~ 49

Author(s):

Martyn V. Bell ◽

Alison E. Cowper ◽

Marie-Paule Lefranc ◽

John I. Bell ◽

Gavin R. Screaton

Keyword(s):

Alternative Splicing ◽

Genomic Structure ◽

Single Gene ◽

Intron Length ◽

Protein Isoforms ◽

Major Influence ◽

Eukaryotic Genes ◽

Alternatively Spliced ◽

Alternatively Spliced Exons

ABSTRACT Although the splicing of transcripts from most eukaryotic genes occurs in a constitutive fashion, some genes can undergo a process of alternative splicing. This is a genetically economical process which allows a single gene to give rise to several protein isoforms by the inclusion or exclusion of sequences into or from the mature mRNA. CD44 provides a unique example; more than 1,000 possible isoforms can be produced by the inclusion or exclusion of a central tandem array of 10 alternatively spliced exons. Certain alternatively spliced exons have been ascribed specific functions; however, independent regulation of the inclusion or skipping of each of these exons would clearly demand an extremely complex regulatory network. Such a network would involve the interaction of many exon-specific trans-acting factors with the pre-mRNA. Therefore, to assess whether the exons are indeed independently regulated, we have examined the alternative exon content of a large number of individual CD44 cDNA isoforms. This analysis shows that the downstream alternatively spliced exons are favored over those lying upstream and that alternative exons are often included in blocks rather than singly. Using a novel in vivo alternative splicing assay, we show that intron length has a major influence upon the alternative splicing of CD44. We propose a kinetic model in which short introns may overcome the poor recognition of alternatively spliced exons. These observations suggest that for CD44, intron length has been exploited in the evolution of the genomic structure to enable tissue-specific patterns of splicing to be maintained.

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