Evolution of Protein Molecules

Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approximately 730-megabase Sorghum bicolor (L.) Moench genome, placing approximately 98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approximately 75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization approximately 70 million years ago, most duplicated gene sets lost one member before the sorghum-rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.

/pdf/the-sorghum-bicolor-genome-and-the-diversification-of-3r9tzdq8e1.pdf

The Sorghum bicolor genome and the diversification of grasses

Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium2, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.

/pdf/the-tomato-genome-sequence-provides-insights-into-fleshy-7a55qpnrdm.pdf

The tomato genome sequence provides insights into fleshy fruit evolution

Sugars not only fuel cellular carbon and energy metabolism but also play pivotal roles as signaling molecules. The experimental amenability of yeast as a unicellular model system has enabled the discovery of multiple sugar sensors and signaling pathways. In plants, different sugar signals are generated by photosynthesis and carbon metabolism in source and sink tissues to modulate growth, development, and stress responses. Genetic analyses have revealed extensive interactions between sugar and plant hormone signaling, and a central role for hexokinase (HXK) as a conserved glucose sensor. Diverse sugar signals activate multiple HXK-dependent and HXKindependent pathways and use different molecular mechanisms to control transcription, translation, protein stability and enzymatic activity. Important and complex roles for Snf1-related kinases (SnRKs), extracellular sugar sensors, and trehalose metabolism in plant sugar signaling are now also emerging.

https://molbio.mgh.harvard.edu/sheenweb/reprints/ARPB06sugar.pdf

Sugar Sensing and Signaling in Plants: Conserved and Novel Mechanisms

The InterPro database (http://www.ebi.ac.uk/interpro/) integrates together predictive models or 'signatures' representing protein domains, families and functional sites from multiple, diverse source databases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY and TIGRFAMs. Integration is performed manually and approximately half of the total approximately 58,000 signatures available in the source databases belong to an InterPro entry. Recently, we have started to also display the remaining un-integrated signatures via our web interface. Other developments include the provision of non-signature data, such as structural data, in new XML files on our FTP site, as well as the inclusion of matchless UniProtKB proteins in the existing match XML files. The web interface has been extended and now links out to the ADAN predicted protein-protein interaction database and the SPICE and Dasty viewers. The latest public release (v18.0) covers 79.8% of UniProtKB (v14.1) and consists of 16 549 entries. InterPro data may be accessed either via the web address above, via web services, by downloading files by anonymous FTP or by using the InterProScan search software (http://www.ebi.ac.uk/Tools/InterProScan/).

/pdf/interpro-the-integrative-protein-signature-database-3vxe9vn1r4.pdf

InterPro: the integrative protein signature database

Wolffia microscopica, a duckweed, flowers in response to a single photoinductive SD cycle of 16 h dark and 8 h light. Flowering in W. microscopica could be induced, under non-inductive long days, by 8-hydroxyquinoline (8-HQ). Flowering was initiated with 10 -6 M 8-HQ and maximum flowering (ca. 75%) was obtained at 5 ×10 -6 M level. Flowering was accentuated further when plants, supplied with 8-HQ, were subjected to SD cycles.

Induction of flowering in a duckweed, Wolffia microscopica, under non-inductive long days, by 8-hydroxyquinoline

Cyclic nucleotide phosphodiesterase from Lemna paucicostata: Effect of Calmodulin and theophylline

Plants have evolved highly sensitive sensory photoreceptor systems to regulate various aspects of their growth and development. Many responses such as seed germination, flowering and dormancy are controlled by red and far-red regions of the solar spectrum through the phytochrome family of photoreceptors. However, several other responses such as stem growth inhibition, phototropism and opening of stomata are controlled by blue and/or ultraviolet light absorbing photoreceptors called cryptochromes and phototropin. Despite their central role in plant biology, the mode of action of these photoreceptors has been shrouded in mystery. Even the biochemical isolation of a photoreceptor, as in the case of phytochrome was accomplished decades ago, did not help in elucidating the mechanism of action. Nevertheless, due to advances in recombinant DNA technology, generation of extensive databanks and the capability to predict function by base sequence analysis, a breakthrough has now come about. It is clear that certain phytochromes, at least in the cyanobacteria and algae which represent the simplest plants, are hybrid photoreceptor-cum-kinases. These novel kinases utilize captured photons rather than conventional ligands to trigger conformational change and in consequence enzyme activity. The kinases apparently, then, cause phosphorylation of many other types of target molecules, leading eventually to various developmental changes. There is suggestive evidence that in higher plants, too, at least some phytochromes may operate as kinases. As compared to work on phytochromes, the blue light photoreceptors have begun to be studied only recently. However, the exciting discovery has been made of at least one photoactive kinase that is critically required for phototropism. This article summarizes the above discoveries from the perspective of general biology.

Novel light-activated protein kinases as key regulators of plant growth and development

Here, we report the draft genome sequence of the hexachlorocyclohexane (HCH)-degrading bacterium Sphingobium ummariense strain RL-3, which was isolated from the HCH dumpsite located in Lucknow, India (27°00′N and 81°09′E). The annotated draft genome sequence (4.75 Mb) of strain RL-3 consisted of 139 contigs, 4,645 coding sequences, and 65% G+C content.

Draft Genome Sequence of Sphingobium ummariense Strain RL-3, a Hexachlorocyclohexane-Degrading Bacterium

After the beginning of the recombinant DNA era in the mid-1970s, researchers in India started to make use of the new technology to understand the structure of plant genes and regulation of their expression. The outcome started to appear in print in early the 1980s and genes for histones, tubulin, photosynthetic membrane proteins, phototransduction components, organelles and those regulated differentially by developmental and extrinsic signals were sequenced and characterized. Some genes of biotechnological importance like those encoding an interesting seed protein and the enzyme glyoxalase were also isolated. While work on the characterization of genome structure and organization was started quite early, it remained largely focused on the identification of DNA markers and genetic variability. In this context, the work on mustard, rice and wheat is worth mentioning. In the year 2000, India became a member of the international consortium to sequence entire rice genome. Several laboratories have also given attention to regulated expression of plastid and nuclear genes as well as to isolate target-specific promoters or design promoters with improved potential. Simultaneously, transgenic systems for crops like mustard, rice, wheat, cotton, legumes and several vegetables have been established. More recently, genes of agronomic importance like those for insect resistance, abiotic stress tolerance, nutritional improvement and male sterility, isolated in India or abroad, have been utilized for raising transgenics for crop improvement. Some of these transgenics have already shown their potential in containment facility or limited field trials conducted under the stipulated guidelines. Plant molecular biology and biotechnology are thus clearly poised to make an impact on research in basic biology and agriculture in the near future.

Jitendra P. Khurana

Papers

Induction of flowering in a duckweed, Wolffia microscopica, under non-inductive long days, by 8-hydroxyquinoline

Cyclic nucleotide phosphodiesterase from Lemna paucicostata: Effect of Calmodulin and theophylline

Novel light-activated protein kinases as key regulators of plant growth and development

Draft Genome Sequence of Sphingobium ummariense Strain RL-3, a Hexachlorocyclohexane-Degrading Bacterium

Plant molecular biology and biotechnology research in the post-recombinant DNA era.