Respiratory metabolism: glycolysis, the TCA cycle and mitochondrial electron transport.

The use of plastic mulch in agriculture has increased dramatically in the last 10 years throughout the world. This increase is due to benefits such as increase in soil temperature, reduced weed pressure, moisture conservation, reduction of certain insect pests, higher crop yields, and more efficient use of soil nutrients. However, disposing of used plastic films, which cause pollution, has led to development of photodegradable and biodegradable mulches. Here we review the use of plastic mulches in agriculture, with special reference to biodegradable mulches. Major topics discussed are (1) history of plastic mulch and impact on crop yield and pest management, (2) limitations of polyethylene mulches and potential alternatives, (3) biodegradable and photodegradable plastic mulches, (4) field performance of biodegradable mulches, and (5) use of biodegradable plastic mulches in organic production. We found that (1) despite multiple benefits, removal and disposal of conventional polyethylene mulches remains a major agronomic, economic, and environmental constraint; (2) early use of photodegradable plastic mulch during the 1970s and 1980s, wrongly named biodegradable mulch films, discouraged adoption of new biodegradable mulch films because they were too expensive and their breakdown was unpredictable; (3) biodegradable plastic films are converted through microbial activity in the soil to carbon dioxide, water, and natural substances; (4) polymers such as poly(lactic acid), poly(butylene adipate-coterephthalate), poly(e-caprolactone), and starch-based polymer blends or copolymers can degrade when exposed to bioactive environments such as soil and compost; (5) with truly biodegradable materials obtained from petroleum and natural resources, opportunity for using biodegradable polymers as agricultural mulch films has become more viable; and (6) the source of polymer and additives may limit use of some biodegradable mulches in organic production. More knowledge is needed on the effect of biodegradable mulches on crop growth, microclimate modifications, soil biota, soil fertility, and yields.

/pdf/polyethylene-and-biodegradable-mulches-for-agricultural-120opw9dwb.pdf

Polyethylene and biodegradable mulches for agricultural applications: a review

https://www.cell.com/molecular-plant/pdf/S1674-2052(15)00366-4.pdf

Amino Acid Catabolism in Plants

Legumes can enter into symbiotic relationships with both nitrogen-fixing bacteria (rhizobia) and mycorrhizal fungi. Nodulation by rhizobia results from a signal transduction pathway induced in legume roots by rhizobial Nod factors. DMI3 ,a Medicago truncatula gene that acts immediately downstream of calcium spiking in this signaling pathway and is required for both nodulation and mycorrhizal infection, has high sequence similarity to genes encoding calcium and calmodulin-dependent protein kinases (CCaMKs). This indicates that calcium spiking is likely an essential component of the signaling cascade leading to nodule development and mycorrhizal infection, and sheds light on the biological role of plant CCaMKs.

Dependent Protein Kinase Required for Bacterial and Fungal Symbioses

Next generation sequencing is transforming our understanding of transcriptomes. It can determine the expression level of transcripts with a dynamic range of over six orders of magnitude from multiple tissues, developmental stages or conditions. Patterns of gene expression provide insight into functions of genes with unknown annotation. The RNA Seq-Atlas presented here provides a record of high-resolution gene expression in a set of fourteen diverse tissues. Hierarchical clustering of transcriptional profiles for these tissues suggests three clades with similar profiles: aerial, underground and seed tissues. We also investigate the relationship between gene structure and gene expression and find a correlation between gene length and expression. Additionally, we find dramatic tissue-specific gene expression of both the most highly-expressed genes and the genes specific to legumes in seed development and nodule tissues. Analysis of the gene expression profiles of over 2,000 genes with preferential gene expression in seed suggests there are more than 177 genes with functional roles that are involved in the economically important seed filling process. Finally, the Seq-atlas also provides a means of evaluating existing gene model annotations for the Glycine max genome. This RNA-Seq atlas extends the analyses of previous gene expression atlases performed using Affymetrix GeneChip technology and provides an example of new methods to accommodate the increase in transcriptome data obtained from next generation sequencing. Data contained within this RNA-Seq atlas of Glycine max can be explored at http://www.soybase.org/soyseq
 .

/pdf/rna-seq-atlas-of-glycine-max-a-guide-to-the-soybean-3ww53gi44f.pdf

RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome.

Biodegradable plastics are those that can be completely degraded in landfills, composters or sewage treatment plants by the action of naturally occurring micro-organisms. Truly biodegradable plastics leave no toxic, visible or distinguishable residues following degradation. Their biodegradability contrasts sharply with most petroleum-based plastics, which are essentially indestructible in a biological context. Because of the ubiquitous use of petroleum-based plastics, their persistence in the environment and their fossil-fuel derivation, alternatives to these traditional plastics are being explored. Issues surrounding waste management of traditional and biodegradable polymers are discussed in the context of reducing environmental pressures and carbon footprints. The main thrust of the present review addresses the development of plant-based biodegradable polymers. Plants naturally produce numerous polymers, including rubber, starch, cellulose and storage proteins, all of which have been exploited for biodegradable plastic production. Bacterial bioreactors fed with renewable resources from plants – so-called ‘white biotechnology’ – have also been successful in producing biodegradable polymers. In addition to these methods of exploiting plant materials for biodegradable polymer production, the present review also addresses the advances in synthesizing novel polymers within transgenic plants, especially those in the polyhydroxyalkanoate class. Although there is a stigma associated with transgenic plants, especially food crops, plant-based biodegradable polymers, produced as value-added co-products, or, from marginal land (non-food), crops such as switchgrass ( Panicum virgatum L.), have the potential to become viable alternatives to petroleum-based plastics and an environmentally benign and carbon-neutral source of polymers.

The second green revolution? Production of plant-based biodegradable plastics.

▪ Abstract Plant cells are unique in that they contain four species of α-ketoacid dehydrogenase complex: plastidial pyruvate dehydrogenase, mitochondrial pyruvate dehydrogenase, α-ketoglutarate (2-oxoglutarate) dehydrogenase, and branched-chain α-ketoacid dehydrogenase. All complexes include multiple copies of three components: an α-ketoacid dehydrogenase/decarboxylase, a dihydrolipoyl acyltransferase, and a dihydrolipoyl dehydrogenase. The mitochondrial pyruvate dehydrogenase complex additionally includes intrinsic regulatory protein-kinase and -phosphatase enzymes. The acyltransferases form the intricate geometric core structures of the complexes. Substrate channeling plus active-site coupling combine to greatly enhance the catalytic efficiency of these complexes. These α-ketoacid dehydrogenase complexes occupy key positions in intermediary metabolism, and a basic understanding of their properties is critical to genetic and metabolic engineering. The current status of knowledge of the biochemical, regul...

THE COMPLEX FATE OF α-KETOACIDS

Plant cells are unique in that they contain four species of alpha-ketoacid dehydrogenase complex: plastidial pyruvate dehydrogenase, mitochondrial pyruvate dehydrogenase, alpha-ketoglutarate (2-oxoglutarate) dehydrogenase, and branched-chain alpha-ketoacid dehydrogenase. All complexes include multiple copies of three components: an alpha-ketoacid dehydrogenase/decarboxylase, a dihydrolipoyl acyltransferase, and a dihydrolipoyl dehydrogenase. The mitochondrial pyruvate dehydrogenase complex additionally includes intrinsic regulatory protein-kinase and -phosphatase enzymes. The acyltransferases form the intricate geometric core structures of the complexes. Substrate channeling plus active-site coupling combine to greatly enhance the catalytic efficiency of these complexes. These alpha-ketoacid dehydrogenase complexes occupy key positions in intermediary metabolism, and a basic understanding of their properties is critical to genetic and metabolic engineering. The current status of knowledge of the biochemical, regulatory, structural, genomic, and evolutionary aspects of these fascinating multienzyme complexes are reviewed.

THECOMPLEXFATE OFα-KETOACIDS

High-throughput peptide mass fingerprinting of soybean seed proteins: automated workflow and utility of UniGene expressed sequence tag databases for protein identification.

Infection of soybean root hairs by Bradyrhizobium japonicum is the first of several complex events leading to nodulation. In the current proteomic study, soybean root hairs after inoculation with B. japonicum were separated from roots. Total proteins were analyzed by two-dimensional (2-D) polyacrylamide gel electrophoresis. In one experiment, 96 protein spots were analyzed by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) to compare protein profiles between uninoculated roots and root hairs. Another 37 spots, derived from inoculated root hairs over different timepoints, were also analyzed by tandem MS (MS/MS). As expected, some proteins were differentially expressed in root hairs compared with roots (e.g., a chitinase and phosphoenolpyruvate carboxylase). Out of 37 spots analyzed by MS/MS, 27 candidate proteins were identified by database comparisons. These included several proteins known to respond to rhizobial inoculation (e.g., peroxidase and phenylalanine-ammonia lyase). However, novel proteins were also identified (e.g., phospholipase D and phosphoglucomutase). This research establishes an excellent system for the study of root-hair infection by rhizobia and, in a more general sense, the functional genomics of a single, plant cell type. The results obtained also indicate that proteomic studies with soybean, lacking a complete genome sequence, are practical.

/pdf/proteomic-analysis-of-soybean-root-hairs-after-infection-by-4q156asabw.pdf

Brian P. Mooney

Papers

The second green revolution? Production of plant-based biodegradable plastics.

THE COMPLEX FATE OF α-KETOACIDS

THECOMPLEXFATE OFα-KETOACIDS

High-throughput peptide mass fingerprinting of soybean seed proteins: automated workflow and utility of UniGene expressed sequence tag databases for protein identification.

Proteomic Analysis of Soybean Root Hairs After Infection by Bradyrhizobium japonicum