Posttranslational Modification of Brain Tubulins from the Antarctic Fish <i>Notothenia coriiceps</i>:  Reduced C-Terminal Glutamylation Correlates with Efficient Microtubule Assembly at Low Temperature

Redeker, Virginie; Frankfurter, Anthony; Sk, Parker; Rossier, Jean; Hw, Detrich

doi:10.1021/bi049070z

Cited by 19 publications

(21 citation statements)

References 36 publications

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“…As with replicate versus consensus comparisons, the 95% CI aids in the use of the spectral dot product because these intervals factor in the number of overlapping peaks to put the dot product into perspective. The finding of no statistical correlation between BTT and the brain spectra is expected; brain tubulin complexity is known to persist across species [19], but tubulin expression and modification patterns differ across tissues within the same species.…”

Section: Resultsmentioning

confidence: 92%

Evaluating reproducibility and similarity of mass and intensity data in complex spectra—applications to tubulin

Olson

Blank

Sackett

et al. 2008

J. Am. Soc. Mass Spectrom.

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We present a data processing approach based on the spectral dot product for evaluating spectral similarity and reproducibility. The method introduces 95% confidence intervals on the spectral dot product to evaluate the strength of spectral correlation; it is the only calculation described to date that accounts for both the non-normal sampling distribution of the dot product and the number of peaks the spectra have in common. These measures of spectral similarity allow for the recursive generation of a consensus spectrum, which incorporates the most consistent features from statistically similar replicate spectra. Taking the spectral dot product and 95% confidence intervals between consensus spectra from different samples yields the similarity between these samples. Applying the data analysis scheme to replicates of brain tubulin CNBr peptides enables a robust comparison of tubulin isotype expression and post-translational modification patterns in rat and cow brains. t is widely recognized that multiple acquisitions of MALDI spectra have extensive variability. Addressing this problem in an automated and robust way becomes vital to the analysis of complex spectra because such spectra often contain peaks that are both inconsistent in their presence or absence and show great variability in intensity. Evaluating differences between replicate spectra manually can be tedious, if not impossible, and automatic tests for discriminating similar and dissimilar spectra have several caveats that have only been partially elaborated to date. Our calculations use the spectral dot product to evaluate spectral similarity. While several papers [1][2][3][4] have used the spectral dot product for evaluating spectral similarity, particularly the similarity of a query spectrum against library references [1, 3, 4], only one paper [4] has addressed the critical issue of how an algorithm or investigator attributes significance to a spectral dot product-a nontrivial detail because the dot product alone can yield equivocal information. Dot product ambiguity arises both from the number of peaks, as has been described [4], and from the different sampling distribution of the dot product at different values. We introduce the 95% confidence intervals on the spectral dot product to address both these sources of ambiguity. To accommodate for spectral variance, multiple acquisitions of the same sample are used to generate a consensus spectrum which incorporates the consistent features from all the replicate spectra. The dot product and its 95% confidence intervals allow for validation of the consensus spectrum by evaluating the similarity of each replicate to the consensus spectrum. The same method is also used to compare and evaluate similarity or dissimilarity between consensus spectra from different sources.Microtubules comprise one of the major fiber systems of the cytoskeleton and are polymers of the heterodimeric protein tubulin. Microtubules and tubulin are present in all eukaryotic cells and are responsible for cellular structure, chromoso...

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Section: Resultsmentioning

confidence: 92%

Evaluating reproducibility and similarity of mass and intensity data in complex spectra—applications to tubulin

Olson

Blank

Sackett

et al. 2008

J. Am. Soc. Mass Spectrom.

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“…the Antarctic Circumpolar Current (ACC) and the Antarctic Polar Front (APF)] of the Southern Ocean. The ACC is located between 50°S and 60°S and is the largest current on Earth in terms of both length and transport capacity (Gordon, 1999 (Detrich et al, 1989(Detrich et al, , 2000Redeker, et al, 2004), the evolution of membranes that maintain their fluidity at cold temperatures, i.e. homeoviscous adaptation (Hazel, 1984;Logue et al, 2000), and the reorganization of metabolic pathways (Crockett and Sidell, 1990;Magnoni et al, 2013) play a significant role in optimizing function at sub-zero temperature.…”

Section: Adaptations To Living In Chronically Frigid Watersmentioning

confidence: 99%

Antarctic notothenioid fish: what are the future consequences of ‘losses’ and ‘gains’ acquired during long-term evolution at cold and stable temperatures?

Beers

Jayasundara

2015

Journal of Experimental Biology

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Antarctic notothenioids dominate the fish fauna of the Southern Ocean. Evolution for millions of years at cold and stable temperatures has led to the acquisition of numerous biochemical traits that allow these fishes to thrive in sub-zero waters. The gain of antifreeze glycoproteins has afforded notothenioids the ability to avert freezing and survive at temperatures often hovering near the freezing point of seawater. Additionally, possession of cold-adapted proteins and membranes permits them to sustain appropriate metabolic rates at exceptionally low body temperatures. The notothenioid genome is also distinguished by the disappearance of traits in some species, losses that might prove costly in a warmer environment. Perhaps the best-illustrated example is the lack of expression of hemoglobin in white-blooded icefishes from the family Channichthyidae. Loss of key elements of the cellular stress response, notably the heat shock response, has also been observed. Along with their attainment of cold tolerance, notothenioids have developed an extreme stenothermy and many species perish at temperatures only a few degrees above their habitat temperatures. Thus, in light of today's rapidly changing climate, it is critical to evaluate how these extreme stenotherms will respond to rising ocean temperatures. It is conceivable that the remarkable cold specialization of notothenioids may ultimately leave them vulnerable to future thermal increases and threaten their fitness and survival. Within this context, our review provides a current summary of the biochemical losses and gains that are known for notothenioids and examines these cold-adapted traits with a focus on processes underlying thermal tolerance and acclimation capacity.

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“…Detrich and colleagues have shown that thermal compensation of microtubule elongation and dynamics in Antarctic fishes results from the evolution of structural changes intrinsic to the α-and β-tubulins (Billger et al, 1994;Detrich et al, 2000;Paluh et al, 2004;Redeker et al, 2004). Miceli et al (2000) have independently defined molecular alterations of the α-and β-tubulins of E. focardii that probably perform the same role.…”

Section: Tubulins Of the Antarctic Ciliate Euplotes Focardii: Insightmentioning

confidence: 99%

Molecular cold-adaptation of protein function and gene regulation: The case for comparative genomic analyses in marine ciliated protozoa

et al. 2009

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Posttranslational Modification of Brain Tubulins from the Antarctic Fish Notothenia coriiceps: Reduced C-Terminal Glutamylation Correlates with Efficient Microtubule Assembly at Low Temperature

Cited by 19 publications

References 36 publications

Evaluating reproducibility and similarity of mass and intensity data in complex spectra—applications to tubulin

Evaluating reproducibility and similarity of mass and intensity data in complex spectra—applications to tubulin

Antarctic notothenioid fish: what are the future consequences of ‘losses’ and ‘gains’ acquired during long-term evolution at cold and stable temperatures?

Molecular cold-adaptation of protein function and gene regulation: The case for comparative genomic analyses in marine ciliated protozoa

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