Tubulin intron sequences: multi‐functional tools

Gianı̀, Silvia; Morello, Laura; Bardini, Mauro; Breviario, Diego

doi:10.1016/s1065-6995(02)00301-3

Cited by 11 publications

(12 citation statements)

References 6 publications

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“…Alternate splicing is not known in tubulin, and thus does not provide a utility to introns. However, regulatory sequences are known to reside in tubulin introns [7,53,54], and if present provide a plausible benefit for intron insertion into established isoforms. Large introns could benefit tubulins, as they reduce Hill-Robertson interference within genes [55].…”

Section: Resultsmentioning

confidence: 99%

Tubulin evolution in insects: gene duplication and subfunctionalization provide specialized isoforms in a functionally constrained gene family

2010

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BackgroundThe completion of 19 insect genome sequencing projects spanning six insect orders provides the opportunity to investigate the evolution of important gene families, here tubulins. Tubulins are a family of eukaryotic structural genes that form microtubules, fundamental components of the cytoskeleton that mediate cell division, shape, motility, and intracellular trafficking. Previous in vivo studies in Drosophila find a stringent relationship between tubulin structure and function; small, biochemically similar changes in the major alpha 1 or testis-specific beta 2 tubulin protein render each unable to generate a motile spermtail axoneme. This has evolutionary implications, not a single non-synonymous substitution is found in beta 2 among 17 species of Drosophila and Hirtodrosophila flies spanning 60 Myr of evolution. This raises an important question, How do tubulins evolve while maintaining their function? To answer, we use molecular evolutionary analyses to characterize the evolution of insect tubulins.ResultsSixty-six alpha tubulins and eighty-six beta tubulin gene copies were retrieved and subjected to molecular evolutionary analyses. Four ancient clades of alpha and beta tubulins are found in insects, a major isoform clade (alpha 1, beta 1) and three minor, tissue-specific clades (alpha 2-4, beta 2-4). Based on a Homarus americanus (lobster) outgroup, these were generated through gene duplication events on major beta and alpha tubulin ancestors, followed by subfunctionalization in expression domain. Strong purifying selection acts on all tubulins, yet maximum pairwise amino acid distances between tubulin paralogs are large (0.464 substitutions/site beta tubulins, 0.707 alpha tubulins). Conversely orthologs, with the exception of reproductive tissue isoforms, show little sequence variation except in the last 15 carboxy terminus tail (CTT) residues, which serve as sites for post-translational modifications (PTMs) and interactions with microtubule-associated proteins. CTT residues overwhelming comprise the co-evolving residues between Drosophila alpha 2 and beta 3 tubulin proteins, indicating CTT specializations can be mediated at the level of the tubulin dimer. Gene duplications post-dating separation of the insect orders are unevenly distributed, most often appearing in major alpha 1 and minor beta 2 clades. More than 40 introns are found in tubulins. Their distribution among tubulins reveals that insertion and deletion events are common, surprising given their potential for disrupting tubulin coding sequence. Compensatory evolution is found in Drosophila beta 2 tubulin cis-regulation, and reveals selective pressures acting to maintain testis expression without the use of previously identified testis cis-regulatory elements.ConclusionTubulins have stringent structure/function relationships, indicated by strong purifying selection, the loss of many gene duplication products, alpha-beta co-evolution in the tubulin dimer, and compensatory evolution in beta 2 tubulin cis-regulation. They evolve through gen...

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Section: Resultsmentioning

confidence: 99%

Tubulin evolution in insects: gene duplication and subfunctionalization provide specialized isoforms in a functionally constrained gene family

2010

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“…1). The correlation between divergent regulation and an additional intron has to be seen in the light of recent findings by Morello et al (2002) and Giani et al (2003). They have shown for tubulin from rice that introns are essential and specific elements for the expression and regulation of tubulin genes.…”

Section: Discussionmentioning

confidence: 98%

A large plant beta-tubulin family with minimal C-terminal variation but differences in expression

Jost¹,

Baur²,

Nick

et al. 2004

Gene

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“…Intron loss and gain are considered by several authors as the main driving force for intron evolution (Blake 1978, Knowles and McLysaght 2006, Roy 2003). The more relaxed evolution of introns has been attributed to the functional role that they can play with regard to gene regulation (Fiume et al 2004, Gianì et al 2003, Rose 2002).…”

Section: Introductionmentioning

confidence: 99%

Intron polymorphism pattern in AOX1b of wild St John's wort (Hypericum perforatum) allows discrimination between individual plants

Ferreira¹,

Cardoso²,

Macedo³

et al. 2009

Physiologia Plantarum

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The present paper deals with the analysis of natural polymorphism in a selected alternative oxidase (AOX) gene of the medicinal plant, St John's wort. Four partial AOX gene sequences were isolated from the genomic DNA of a wild plant of Hypericum perforatum L. Three genes belong to the subfamily AOX1 (HpAOX1a, b and c) and one to the subfamily AOX2 (HpAOX2). The partial sequence of HpAOX1b showed polymerase chain reaction (PCR) fragment size variation as a result of variable lengths in two introns. PCR performed by Exon Primed Intron Crossing (EPIC)-PCR displayed the same two-band pattern in six plants from a collection. Both fragments showed identical sequences for all exons. However, each of the two introns showed an insertion/deletion (InDel) in identical positions for all plants that counted for the difference in the two fragment sizes. The InDel in intron 1 influenced the predictability of a pre-microRNA site. The almost identical PCR fragment pattern was characterized by a high variability in the sequences. The InDels in both introns were linked to repetitive intron single nucleotide polymorphisms (ISNP)s. The polymorphic pattern obtained by InDels and ISNPs from both fragments together was appropriate to discriminate between all individual plants. We suggest that AOX sequence polymorphism in H. perforatum can be used for studies on gene diversity and biodiversity. Further, we conclude that AOX sequence polymorphism of individual plants should be considered in biological studies on AOX activity to exclude the influence of genetic diversity. The identified polymorphic fragments are available to be explored in future experiments as a potential source for functional marker development related to the characterization of origins/accessions and agronomic traits such as plant growth, development and yield stability.

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Tubulin intron sequences: multi‐functional tools

Cited by 11 publications

References 6 publications

Tubulin evolution in insects: gene duplication and subfunctionalization provide specialized isoforms in a functionally constrained gene family

Tubulin evolution in insects: gene duplication and subfunctionalization provide specialized isoforms in a functionally constrained gene family

A large plant beta-tubulin family with minimal C-terminal variation but differences in expression

Intron polymorphism pattern in AOX1b of wild St John's wort (Hypericum perforatum) allows discrimination between individual plants

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