An alternative,zeaxanthin epoxidase-independent abscisic acid biosynthetic pathway in plants

Abscisic acid(ABA)is an important carotenoid-derived phytohormone that plays essential roles in plant response to biotic and abiotic stresses as well as in various physiological and developmental processes.In Arabidopsis,ABA biosynthesis starts with the epoxidation of zeaxanthin by the ABA DEFICIENT 1(ABA1)enzyme,leading to epoxycarotenoids;e.g.,violaxanthin.The oxidative cleavage of 9-cis-epoxycaro-tenoids,a key regulatory step catalyzed by 9-C/S-EPOXYCAROTENOID DIOXYGENASE,forms xanthoxin,which is converted in further rea.ctions mediated by ABA DEFICIENT 2(ABA2),ABA DEFICIENT 3(ABA3),and ABSCISIC ALDEHYDE OXIDASE 3(AAO3)into ABA.By combining genetic and biochemical approaches,we unravel here an ABA1-independent ABA biosynthetic pathway starting upstream of zeaxanthin.We iden-tified the carotenoid cleavage products(i.e.,apocarotenoids,β-apo-11-carotenal,9-cis-β-apo-11-carotenal,3-OH-β-apo-11-carotenal,and 9-cis-3-OH-β-apo-11-carotenal)as intermediates of this ABA1-independent ABA biosynthetic pathway.Using labeled compounds,we showed thatβ-apo-11-carotenal,9-cis-β-apo-11-carotenal,and 3-OH-β-apo-11-carotenal are successively converted into 9-cis-3-OH-β-apo-11-carotenal,xanthoxin,and finally into ABA in both Arabidopsis and rice.When applied to Arabidopsis,theseβ-apo-11-carotenoids exert ABA biological functions,such as maintaining seed dormancy and inducing the expression of ABA-responsive genes.Moreover,the transcdptomic analysis revealed a high overlap of differentially expressed genes regulated byβ-apo-11-carotenoids and ABA,suggesting thatβ-apo-11-carot-enoids exert ABA-independent regulatory activities.Taken together,our study identifies a biological function for the common plant metabolites,β-apo-11-carotenoids,extends our knowledge about ABA biosynthesis,and provides new insights into plant apocarotenoid metabolic networks.

Marine Metagenome as A Resource for Novel Enzymes

More than 99% of identified prokaryotes, including many from the marine environment, cannot be cultured in the laboratory. This lack of capability restricts our knowledge of microbial genetics and community ecology. Metagenomics, the culture-independent cloning of environmental DNAs that are isolated directly from an environmental sample, has already provided a wealth of information about the uncultured microbial world. It has also facilitated the discovery of novel bio- catalysts by allowing researchers to probe directly into a huge diversity of enzymes within natural microbial communities. Recent advances in these studies have led to a great interest in recruiting microbial enzymes for the development of environmentally-friendly industry. Although the metage- nomics approach has many limitations, it is expected to provide not only scientific insights but also economic benefits, especially in industry. This review highlights the importance of metagenomics in mining microbial lipases, as an example, by using high-throughput techniques. In addition, we dis- cuss challenges in the metagenomics as an important part of bioinformatics analysis in big data.

Integration of Droplet Microfluidic Tools for Single-cell Functional Metagenomics:An Engineering Head Start

Droplet microfluidic techniques have shown promising outcome to study single cells at high throughput.However,their adoption in laboratories studying“-omics”sciences is still irrelevant due to the complex and multidisciplinary nature of the field.To facilitate their use,here we provide engineering details and organized protocols for integrating three droplet-based microfluidic technologies into the metagenomic pipeline to enable functional screening of bioproducts at high throughput.First,a device encapsulating single cells in droplets at a rate of~250 Hz is described considering droplet size and cell growth.Then,we expand on previously reported fluorescence-activated droplet sorting systems to integrate the use of 4 independent fluorescence-exciting lasers(i.e.,405,488,561,and 637 nm)in a single platform to make it compatible with different fluorescence-emitting biosensors.For this sorter,both hardware and software are provided and optimized for effortlessly sorting droplets at 60 Hz.Then,a passive droplet merger is also integrated into our pipeline to enable adding new reagents to already-made droplets at a rate of 200 Hz.Finally,we provide an optimized recipe for manufacturing these chips using silicon dry-etching tools.Because of the overall integration and the technical details presented here,our approach allows biologists to quickly use microfluidic technologies and achieve both single-cell resolution and high-throughput capability(>50,000 cells/day)for mining and bioprospecting metagenomic data.

In Memory of Vladimir B.Bajic(1952–2019)

Professor Vladimir B.Bajic,a world-renowned pioneer in bioinformatics and associate editor-in-chief of Genomics Proteomics&Bioinformatics(GPB)since 2015,passed away on31 October 2019 in Jeddah,Saudi Arabia.Prof.Bajic joined the editorial board of GPB in 2012 and had been devoting his precious time and efforts to handling and reviewing manuscripts and providing many valuable instructions and suggestions in improving journal quality and readership as well.