Intragenic tandem repeats generate functional variability

Verstrepen, Kevin J.; Jansen, An; Lewitter, Fran; Fink, Gerald R.

doi:10.1038/ng1618

Cited by 565 publications

(655 citation statements)

References 29 publications

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“…Evidence of tandem gene duplication and high levels of polymorphism suggests that spidroins are naturally selected to maintain diversity. The presence of long arrays of tandem repeats in spidroins, reminiscent of those that facilitate rapid variation on microbial cell surfaces 61 and morphological plasticity in mammals 62 , also suggests a gene family undergoing continuous evolution. In particular, N. clavipes spidroin gene phylogenies ( Fig.…”

Section: Discussionmentioning

confidence: 99%

The Nephila clavipes genome highlights the diversity of spider silk genes and their complex expression

et al. 2017

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More than 380 million years of evolution have produced >46,000 extant spider species, exhibiting an incredible diversity of silks used for prey capture and reproduction [1][2][3] . Spider silks can be stronger than steel and tougher than Kevlar, yet are much lighter weight than these manmade materials 4 . Silks vary in extensibility 5 , are temperature resilient 6 , can enable electrical conduction 7 , and can inhibit bacterial growth while being nearly invisible to the human immune system 8 . Thus, novel materials derived from spider silks offer tremendous potential for medical and industrial innovation. To take advantage of their desirable properties, we must learn more about spider silk genetic structure, functional diversity, and production.A female orb-weaving spider can have up to seven morphologically differentiated types of silk glands, each believed to extrude a distinct class of silk with biophysical characteristics resulting from the expression of a unique combination of silk genes in that gland 9,10 . The silk classes of a typical 'gluey silk' orb-weaver (Araneoidea) female include (i) major ampullate silk, which exhibits great tensile strength and is employed in draglines, bridgelines, and web radii 11,12 ; (ii) minor ampullate silk, used for inelastic temporary spirals during web building 11,12 ; (iii) cement-like piriform silk that bonds fibers together and to other substrates 13,14 ; (iv) strong, yet flexible aciniform silk used for prey wrapping and egg case insulation 15 ; (v) tubuliform and cylindriform silk that constitutes the tough outer layer of egg cases 16,17 ; (vi) flagelliform silk that exhibits unparalleled extensibility and is used in the capture spiral 18,19 ; and (vii) the viscous and sticky aggregate silk that aids in prey capture [20][21][22][23][24] . Many spider species produce just a subset of these silk classes, and some produce yet other silk types, including cribellate silk 25 . Each species possesses an assortment of specialized gland types that are thought to produce distinct classes of silks to fit specific needs 9,26,27 .Spider silks are composed primarily of spidroin proteins (where a 'spidroin' is a spider fibroin [28][29][30][31] ) that, by convention, have been named and classified according to the specific silk gland in which they were first discovered. Spidroin proteins have conserved N-and C-terminal domains that flank long runs of repeated motifs 32-34 , the composition and number of which confer specific physical properties to silks 27 . Yet, despite decades of research on orb-weaver silks, there is incomplete knowledge of all the spidroins within an orb-weaver species.Adding to the sampling of sequences obtained from targeted investigations, the assembly of the velvet spider (Stegodyphus mimosarum) genome yielded 19 spidroins, the largest collection from any single species 27 . Owing to the challenges of assembling arrays of repeats, several of the S. mimosarum spidroin sequences are incomplete, without the sequences encoding N-and C-terminal domains anchored ...

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Section: Discussionmentioning

confidence: 99%

The Nephila clavipes genome highlights the diversity of spider silk genes and their complex expression

et al. 2017

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“…Such changes are believed to be facilitated by the nature of the genes responsible for flocculation in yeast strains, which contain many tandem repeats 52 and are consequently highly susceptible to mutation without causing a loss in viability 42,51 . Analysis of flocculation using the Helms assay revealed that BridgePort lager yeast was moderately flocculent (41.45 ± 8.67) when grown in synthetic media (YPD), while the ale strain was more strongly flocculent (86.0 ± 6.4).…”

Section: Effect Of Extended Serial Repitching On Yeast Flocculation Cmentioning

confidence: 99%

Long Term Serial Repitching and the Genetic and Phenotypic Stability of Brewer's Yeast

Powell

Diacetis²

2007

Journal of the Institute of Brewing

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Two brewing yeast strains, one employed for the production of an ale type product and the other used solely for bottle conditioning, were serially repitched over a period of one year. Subsequently each yeast culture was compared to the original stocks for a variety of phenotypic and genotypic characteristics. Fermentation performance was assessed in terms of flocculation capacity and the time required to achieve attenuation in 150 barrel fermentation vessels, while the propensity for the population to accumulate variants was assessed by analysing giant colony morphology. Changes to the genome were monitored by DNA fingerprinting of each yeast culture using RAPD-PCR and RFLP. Although some colony morphology variation was observed between fresh and old ale yeast cultures, there were no detectable genetic changes or alterations in fermentation characteristics to either yeast strain over the course of serial repitching. It is suggested that although some brewing yeast strains are susceptible to genetic drift, others are more resilient and can remain stable over extended periods of time. The propensity to produce variants may therefore play a significant role in determining the number of times a strain may be serially repitched, or its suitability for beer fermentations.

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“…They enable rearrangements both between and within flocculin genes. Several studies have shown that the longer the Flo protein (carrying more repeats) the stronger is the flocculation ability it confers 30,105,111 . Accordingly, FLO1 was observed to be the longest FLO gene, with the most repeats and to confer the strongest flocculation phenotype 104 .…”

Section: The Flo Family Genes Are Unstablementioning

confidence: 99%

“…FLO genes are very long (up to 4.6 kbp) because of tandem repeated DNA sequences of about 100 nucleotides that are repeated 10-20 times in each gene 104,105 . Tandem repeated DNA sequences in the FLO genes are highly dynamic components of the genome, i.e.…”

Section: The Flo Family Genes Are Unstablementioning

confidence: 99%

125th Anniversary Review: Yeast Flocculation and Sedimentation in Brewing

Vidgren

Londesborough

2011

Journal of the Institute of Brewing

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Flocculation is prerequisite for bulk sedimentation of yeast during brewery fermentation. Although single yeast cells gradually sediment in green beer, this sedimentation rate is too slow without formation of large yeast flocs. The present review concerns the major determinants of yeast flocculation and sedimentation in brewery fermentations. Flocculation characteristics of yeast are strongly strain-dependent and largely defined by which FLO genes are functional in each strain. In addition to the genetic background, several environmental factors affect flocculation. These can be, somewhat arbitrarily, classified as physiological factors, such as the calcium availability, pH, temperature and ethanol and oxygen concentrations in the medium or physical factors, such as cell surface hydrophobicity, cell surface charge and the presence of appropriate hydrodynamic conditions for the formation of large flocs. Once yeast flocs are formed, their size, shape and density and the properties of the surrounding medium affect the rate at which the flocs sediment. Higher gravity worts usually result in green beers with higher viscosity and density, which both retard sedimentation. Moreover, environmental factors during yeast handling before fermentation, e.g., propagation, storage and cropping, influence the flocculation potential of yeast in subsequent fermentation. Premature yeast flocculation (PYF) and the role of PYF factors are discussed. In conclusion, some potential options available to adjust yeast flocculation are described.

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Intragenic tandem repeats generate functional variability

Cited by 565 publications

References 29 publications

The Nephila clavipes genome highlights the diversity of spider silk genes and their complex expression

The Nephila clavipes genome highlights the diversity of spider silk genes and their complex expression

Long Term Serial Repitching and the Genetic and Phenotypic Stability of Brewer's Yeast

125th Anniversary Review: Yeast Flocculation and Sedimentation in Brewing

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