Table of Contents

Volume 3, Issue 3

  May/June 2012

View covers archive

LANDES HIGHLIGHTS

Landes Highlights

Margit Pacher-Zavisin
http://dx.doi.org/10.4161/bbug.20136
PDF




NEWS AND VIEWS

Ferretting out the facts behind the H5N1 controversy

Roy D. Sleator
http://dx.doi.org/10.4161/bbug.19943
Abstract | Full Text | PDF

Recent recommendations by the National Science Advisory Board for Biosecurity (NSABB) to redact key methodological details of two studies involving mammal-to-mammal transmission of the H5N1 (H5) subtype influenza viruses, has led to a temporary moratorium on all research involving live H5N1 or H5 HA reassortant viruses shown to be transmissible in ferrets. Herein, I review the events which led to this impasse and comment on their impact.




LETTER TO THE EDITOR

H5N1 moratorium: Missing the point

Pat G. Casey
http://dx.doi.org/10.4161/bbug.20004
Abstract | Full Text | PDF

The recent moratorium on research using engineered H5N1 influenza viruses is a move which cannot achieve its aims as it ignores the prevalence of molecular biology.

Avian H5N1 influenza: In or out flew-enza?

John G. Morgan
http://dx.doi.org/10.4161/bbug.20190
PDF




REVIEW

Open Access Article

The winemaker’s bug: From ancient wisdom to opening new vistas with frontier yeast science

Isak S. Pretorius, Christopher D. Curtin and Paul Chambers
http://dx.doi.org/10.4161/bbug.19687
Abstract | Full Text | PDF

The past three decades have seen a global wine glut. So far, well-intended but wasteful and expensive market-intervention has failed to drag the wine industry out of a chronic annual oversupply of roughly 15%. Can yeast research succeed where these approaches have failed by providing a means of improving wine quality, thereby making wine more appealing to consumers? To molecular biologists Saccharomyces cerevisiae is as intriguing as it is tractable. A simple unicellular eukaryote, it is an ideal model organism, enabling scientists to shed new light on some of the biggest scientific challenges such as the biology of cancer and aging. It is amenable to almost any modification that modern biology can throw at a cell, making it an ideal host for genetic manipulation, whether by the application of traditional or modern genetic techniques. To the winemaker, this yeast is integral to crafting wonderful, complex wines from simple, sugar-rich grape juice. Thus any improvements that we can make to wine yeast fermentation performance or the sensory properties it imparts to wine will benefit winemakers and consumers. With this in mind, the application of frontier technologies, particularly the burgeoning fields of systems and synthetic biology, have much to offer in their pursuit of “novel” yeast strains to produce high quality wine. This paper discusses the nexus between yeast research and winemaking. It also addresses how winemakers and scientists face up to the challenges of consumer perceptions and opinions regarding the intervention of science and technology; the greater this intervention, the stronger the criticism that wine is no longer “natural”. How can wine researchers respond to the growing number of wine commentators and consumers who feel that scientific endeavors favor wine quantity over quality, and “technical sophistication, fermentation reliability and product consistency” over “artisanal variation”? This paper seeks to present yeast research in a new light and a new context, and it raises important questions about the direction of yeast research, its contribution to science and the future of winemaking.




REPORT

Identification of iron-regulated genes of Bifidobacterium breve UCC2003 as a basis for controlled gene expression

Michelle Cronin, Aldert Zomer, Gerald Fitzgerald and Douwe van Sinderen
http://dx.doi.org/10.4161/bbug.18985
Abstract | Full Text | PDF

Iron is an essential growth factor for virtually all organisms. However, iron is not readily available in most environments and microorganisms have evolved specialized mechanisms, such as the use of siderophores and high-affinity transport systems, to acquire iron when confronted with iron-limiting conditions. In general these systems are tightly regulated to prevent iron-induced toxicity and because they are quite costly to the microbe. Because of this tight regulation we chose to explore the response of Bifidobacterium breve UCC2003 to iron limitation. Through microarray and complementation analyses we identified and characterized a presumed ferrous iron uptake system, encoded by bfeUOB, from B. breve UCC2003 and exploited its regulated transcription to develop an inducible expression system for use in bifidobacteria.




TECHNICAL PAPERS

The Saccharomyces cerevisiae SCRaMbLE system and genome minimization

Jessica Dymond and Jef Boeke
http://dx.doi.org/10.4161/bbug.19543
Abstract | PDF

We have recently reported the first partially synthetic eukaryotic genome. Saccharomyces cerevisiae chromosomes synIXR and semi-synVIL are fully synthetic versions of the right arm of chromosome IX and the telomeric segment of the left arm of chromosome VI, respectively, and represent the beginning of the synthetic yeast genome project, Sc2.0, that progressively replaces native yeast DNA with synthetic sequences. We have designed synthetic chromosome sequences according to principles specifying a wild-type phenotype, highly stable genome, and maintenance of genetic flexibility. Although other synthetic genome projects exist, the Sc2.0 approach is unique in that we have implemented design specifications predicted to generate a wild-type phenotype until induction of “SCRaMbLE,” an inducible evolution system that generates significant genetic diversity. Here we further explore the significance of Sc2.0 and show how SCRaMbLE can serve as a genome minimization tool.

Saccharomyces cerevisiae in directed evolution: An efficient tool to improve enzymes

David Gonzalez-Perez, Eva Garcia-Ruiz and Miguel Alcalde
http://dx.doi.org/10.4161/bbug.19544
Abstract | PDF

Over the past 20 years, directed evolution has been seen to be the most reliable approach to protein engineering. Emulating the natural selection algorithm, ad hoc enzymes with novel features can be tailor-made for practical purposes through iterative rounds of random mutagenesis, DNA recombination and screening. Of the heterologous hosts used in laboratory evolution experiments, the budding yeast Saccharomyces cerevisiae has become the best choice to express eukaryotic proteins with improved properties. S. cerevisiae not only allows mutant enzymes to be secreted but also, it permits a wide range of genetic manipulations to be employed, ranging from in vivo cloning to the creation of greater molecular diversity, thanks to its efficient DNA recombination apparatus. Here, we summarize some successful examples of the use of the S. cerevisiae machinery to accelerate artificial evolution, complementing the traditional in vitro methods to generate tailor-made enzymes.




ADDENDA

Saccharomyces cerevisiae STR3 and yeast cystathionine β-lyase enzymes: The potential for engineering increased flavor release

Sylvester Holt, Antonio Cordente and Chris Curtin
http://dx.doi.org/10.4161/bbug.19566
Abstract | PDF

Selected Saccharomyces cerevisiae strains are used for wine fermentation. Based on several criteria, winemakers often use a specific yeast to improve the flavor, mouth feel, decrease the alcohol content and desired phenolic content, just to name a few properties. Scientists at the AWRI previously illustrated the potential for increased flavor release from grape must via overexpression of the Escherichia coli Tryptophanase enzyme in wine yeast. To pursue a self-cloning approach for improving the aroma production, we recently characterized the S. cerevisiae cystathionine β-lyase STR3, and investigated its flavor releasing capabilities. Here, we continue with a phylogenetic investigation of STR3 homologs from non-Saccharomyces yeasts to map the potential for using natural variation to engineer new strains.

Frex and FrexH: Indicators of metabolic states in living cells

Yuzheng Zhao and Yi Yang
http://dx.doi.org/10.4161/bbug.19769
Abstract | PDF

Reduced nicotinamide adenine dinucleotide (NADH) and its oxidized form play central roles in energy and redox metabolisms. For many years, researchers have relied on the weak NADH endogenous fluorescence signal to determine the NADH level in living cells. We recently reported a series of genetically encoded fluorescent sensors highly specific for NADH. These sensors allow real-time, quantitative measurement of this significant molecule in different subcellular compartments. In this study, we provide a more detailed discussion of the benefits and limitations of these genetically encoded fluorescent sensors. These sensors are utilized in most laboratories without the need for sophisticated instruments because of their superior sensitivity and specificity. They are also viable alternatives to existing techniques for measuring the endogenous fluorescence of intracellular NAD(P)H.