NUPTs in Sequenced Eukaryotes and Their Genomic Organization in Relation to NUMTs

NUPTs (nuclear plastid DNA) derive from plastid-to-nucleus DNA transfer and exist in various plant species. Experimental data imply that the DNA transfer is an ongoing, highly frequent process, but for the interspecific diversity of NUPTs, no clear explanation exists. Here, an inventory of NUPTs in the four sequenced plastid-bearing species and their genomic organization is presented. Large genomes with a predicted low gene density contain more NUPTs. In Chlamydomonas and Plasmodium, DNA transfer occurred but was limited, probably because of the presence of only one plastid per cell. In Arabidopsis and rice, NUPTs are frequently organized as clusters. Tight clusters can contain both NUPTs and NUMTs (nuclear mitochondrial DNA), indicating that preNUPTs and preNUMTs might have concatamerized before integration. The composition of such a hypothetical preNUPT-preNUMT pool seems to be variable, as implied by substantially different NUPTs:NUMTs ratios in different species. Loose clusters can span several dozens of kbps of nuclear DNA, and they contain markedly more NUPTs or NUMTs than expected from a random genomic distribution of nuclear organellar DNA. The level of sequence similarity between NUPTs/NUMTs and plastid/mitochondrial DNA correlates with the size of the integrant. This implies that original insertions are large and decay over evolutionary time into smaller fragments with diverging sequences. We suggest that tight and loose clusters represent intermediates of this decay process

NUMTs in Sequenced Eukaryotic Genomes

Mitochondrial DNA sequences are frequently transferred to the nucleus giving rise to the so-called nuclear mitochondrial DNA (NUMT). Analysis of 13 eukaryotic species with sequenced mitochondrial and nuclear genomes reveals a large interspecific variation of NUMT number and size. Copy number ranges from none or few copies in Anopheles, Caenorhabditis, Plasmodium, Drosophila, and Fugu to more than 500 in human, rice, and Arabidopsis. The average size is between 62 (baker’s yeast) and 647 bps (Neurospora), respectively. A correlation between the abundance of NUMTs and the size of the nuclear or the mitochondrial genomes, or of the nuclear gene density, is not evident. Other factors, such as the number and/or stability of mitochondria in the germline, or species-specific mechanisms controlling accumulation/loss of nuclear DNA, might be responsible for the interspecific diversity in NUMT accumulation

Mode of Amplification and Reorganization of Resistance Genes During Recent Arabidopsis thaliana Evolution

The NBS-LRR (nucleotide-binding site plus leucine-rich repeat) genes represent the major class of disease resistance genes in flowering plants and comprise 166 genes in the ecotype Col-0 of Arabidopsis thaliana. NBS-LRR genes are organized in single-gene loci, clusters, and superclusters. Phylogenetic analysis reveals nine monophyletic clades and a few phylogenetic orphans. Most clusters contain only genes from the same phylogenetic lineage, reflecting their origin from the exchange of sequence blocks as a result of intralocus recombination. Multiple duplications increased the number of NBS-LRR genes in the progenitors of Arabidopsis, suggesting that the present complexity in Col-0 may derive from as few as 17 progenitors. The combination of physical and phylogenetic analyses of the NBS-LRR genes makes it possible to detect relatively recent gene rearrangements, which increased the number of NBS-LRR genes by about 50, but which are almost never associated with large segmental duplications. The identification of 10 heterogeneous clusters containing members from different clades demonstrates that sequence sampling between different resistance gene loci and clades has occurred. Such events may have taken place early during flowering plant evolution, but they generated modules that have been duplicated and remobilized also more recently

Evolutionary tinkering: birth of a novel chloroplast protein

The term ‘evolutionary tinkering’ refers to evolutionary innovation by recombination of functional units, and includes the creation of novel proteins from pre-existing modules. A novel instance of evolutionary tinkering was recently discovered in the flowering plant genus Nicotiana: the conversion of a nuclear transcription factor into the plastid-resident protein WIN4 (wound-induced clone 4) involved in environmental stress responses. In this issue of the Biochemical Journal, Kodama and Sano now show that two steps are necessary for the establishment of the novel plastid protein: the acquisition of an internal translation initiation site and the use of multiple transcription starts to produce short mRNA variants that encode the plastid-targeted protein form

Structural and Functional Genomics in Semi-Autonomous Organelles: Composition and Origin of Proteomes of Chloroplasts and Mitochondria and Related Transcriptomics

Mitochondria and chloroplasts are semi-autonomous organelles that have arisen through an endosymbiotic event and, over evolutionary time, have donated most of their genome to the nucleus of the host cell. Due to this transfer of genetic material, the expression of many proteins of the organellar proteomes, now synthesized in the cytosol and re-targeted to the organelles, came under control of the nucleus. Subsequently, means of communication between organelles and nucleus must exist, enabling the organelles to take influence on the nuclear gene expression. This thesis focused on structural and functional genomics in mitochondria and chloroplasts, addressing questions related to the composition, origin and evolution of the organelles, as well as, chloroplast-to-nucleus signaling. The accuracy of five different predictors for the detection of N-terminal targeting peptides was evaluated employing test sets consisting of proteins with experimentally proven subcellular localization, and found to be substantially lower than reported before. Combinations of the predictors showed to be more accurate than any of the predictors alone and were subsequently used to estimate the size and composition of the organellar proteomes. A prediction of the mitochondrial proteomes for ten species was performed and revealed that functional mitochondria harbor from a few hundred to more than 3,000 gene products. A core set of conserved mitochondrial proteins could be identified whose functions are mostly related to transport and metabolism, and -- if mutated -- are frequently associated with disease in humans. In collaboration with W. Martin (Universität Düsseldorf) and co-workers, the cyanobacterial heritage of the Arabidopsis genome was estimated by phylogenetic inferrence and about 4,800 genes (or 18% of the genome) were shown to have been acquired from the prokaryotic ancestor. In both flowering plants, A. thaliana and O. sativa, about 7% of the whole proteome were predicted to be targeted to the chloroplast, with close to 600 of those proteins shared by both species and most likely to be derived from cyanobacteria. The functions of this subset are mainly related to metabolism and energy. In both organelles, species-specific proteins were detected indicating a functional diversification. Even though in A. thaliana the cTP-featuring proteins are predominantly of prokaryotic origin (more than 50%), this indicates that post-endosymbiotic relocations of proteins from/to the chloroplast occurred by altered targeting. These findings were also confirmed for mitochondria. A differential-expression analysis of the nuclear chloroplast transcriptome under 35 environmental and genetic conditions was performed. It revealed, that most of those conditions elicit only three main classes of transcriptome response. Two of these classes, probably involving GUN-type plastid signaling, are characterized by alterations, in opposite directions, in the expression of largely overlapping sets of genes. Thus these findings, suggest the existence of a regulatory, binary master-switch

The role of CDC48 in the retro-translocation of non-ubiquitinated toxin substrates in plant cells

When the catalytic A subunits of the castor bean toxins ricin and Ricinus communis agglutinin (denoted as RTA and RCA A, respectively) are delivered into the endoplasmic reticulum (ER) of tobacco protoplasts, they become substrates for ER-associated protein degradation (ERAD). As such, these orphan polypeptides are retro-translocated to the cytosol, where a significant proportion of each protein is degraded by proteasomes. Here we begin to characterise the ERAD pathway in plant cells, showing that retro-translocation of these lysine-deficient glycoproteins requires the ATPase activity of cytosolic CDC48. Lysine polyubiquitination is not obligatory for this step. We also show that while RCA A is found in a mannose-untrimmed form prior to its retro-translocation, a significant proportion of newly synthesised RTA cycles via the Golgi and becomes modified by downstream glycosylation enzymes. Despite these differences, both proteins are similarly retro-translocated

Big Data Analytics Capabilities: A Systematic Literature Review on Necessary Skills to Succeed in Big Data Analytics

While the amount of data keeps growing, managers ask themselves whether they already retrieve full value from their data. To maximize the value of big data, literature offers first insights in building BDA capabilities (Gupta and George 2016, p; Mikalef et al. 2018). Nevertheless, BDA remains a new field to researchers and companies. BDA frameworks, still offered scarcely, discuss roughly the same dimensions (incorporating some technical, human, and cultural aspects), but are only superficially discussed. This thesis builds a framework of the different approaches offered in literature. Furthermore, it is important to distinguish whether a new development as BDA can be seen as a trend topic or rather a long-lasting game changer for businesses. Here, this thesis discusses differences among digital capabilities, IT capabilities, that research stared addressing by 1990, and BDA capabilities. A major finding is that building IT capabilities is considered as an isolated responsibility of IT departments by, i.e., offering IT infrastructure to the whole company. BDA capabilities, on the contrary, cannot be planned and rolled out from one specific department – those need to be developed in every organizational unit; therefore, a data-driven culture is a key element in building BDA capabilities. Keywords: Big data analytics; Big data; Data analytics; Dynamic capabilities; Resource-based view.While the amount of data keeps growing, managers ask themselves whether they already retrieve full value from their data. To maximize the value of big data, literature offers first insights in building BDA capabilities (Gupta and George 2016, p; Mikalef et al. 2018). Nevertheless, BDA remains a new field to researchers and companies. BDA frameworks, still offered scarcely, discuss roughly the same dimensions (incorporating some technical, human, and cultural aspects), but are only superficially discussed. This thesis builds a framework of the different approaches offered in literature. Furthermore, it is important to distinguish whether a new development as BDA can be seen as a trend topic or rather a long-lasting game changer for businesses. Here, this thesis discusses differences among digital capabilities, IT capabilities, that research stared addressing by 1990, and BDA capabilities. A major finding is that building IT capabilities is considered as an isolated responsibility of IT departments by, i.e., offering IT infrastructure to the whole company. BDA capabilities, on the contrary, cannot be planned and rolled out from one specific department – those need to be developed in every organizational unit; therefore, a data-driven culture is a key element in building BDA capabilities. Keywords: Big data analytics; Big data; Data analytics; Dynamic capabilities; Resource-based view

Proteomic Analysis of Chloroplast-to-Chromoplast Transition in Tomato Reveals Metabolic Shifts Coupled with Disrupted Thylakoid Biogenesis Machinery and Elevated Energy-Production Components

A comparative proteomic approach was performed to identify differentially expressed proteins in plastids at three stages of tomato(Solanum lycopersicum) fruit ripening (mature-green, breaker, red). Stringent curation and processing of the data from three independent replicates identified 1,932 proteins among which 1,529 were quantified by spectral counting. The quantification procedures have been subsequently validated by immunoblot analysis of six proteins representative of distinct metabolic or regulatory pathways. Among the main features of the chloroplast-to-chromoplast transition revealed by the study, chromoplastogenesis appears to be associated with major metabolic shifts: (1) strong decrease in abundance of proteins of light reactions (photosynthesis, Calvin cycle, photorespiration)and carbohydrate metabolism (starch synthesis/degradation), mostly between breaker and red stages and (2) increase in terpenoid biosynthesis (including carotenoids) and stress-response proteins (ascorbate-glutathione cycle, abiotic stress, redox, heat shock). These metabolic shifts are preceded by the accumulation of plastid-encoded acetyl Coenzyme A carboxylase D proteins accounting for the generation of a storage matrix that will accumulate carotenoids. Of particular note is the high abundance of proteins involved in providing energy and in metabolites import. Structural differentiation of the chromoplast is characterized by a sharp and continuous decrease of thylakoid proteins whereas envelope and stroma proteins remain remarkably stable. This is coincident with the disruption of the machinery for thylakoids and photosystem biogenesis (vesicular trafficking, provision of material for thylakoid biosynthesis, photosystems assembly) and the loss of the plastid division machinery. Altogether, the data provide new insights on the chromoplast differentiation process while enriching our knowledge of the plant plastid proteome

A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes

Analyses of 55 individual and 31 concatenated protein data sets encoded in Reclinomonas americana and Marchantia polymorpha mitochondrial genomes revealed that current methods for constructing phylogenetic trees are insufficiently sensitive (or artifact-insensitive) to ascertain the sister of mitochondria among the current sample of eight alpha-proteobacterial genomes using mitochondrially-encoded proteins. However, Rhodospirillum rubrum came as close to mitochondria as any alpha-proteobacterium investigated. This prompted a search for methods to directly compare eukaryotic genomes to their prokaryotic counterparts to investigate the origin of the mitochondrion and its host from the standpoint of nuclear genes. We examined pairwise amino acid sequence identity in comparisons of 6,214 nuclear protein-coding genes from Saccharomyces cerevisiae to 177,117 proteins encoded in sequenced genomes from 45 eubacteria and 15 archaebacteria. The results reveal that approximately 75% of yeast genes having homologues among the present prokaryotic sample share greater amino acid sequence identity to eubacterial than to archaebacterial homologues. At high stringency comparisons, only the eubacterial component of the yeast genome is detectable. Our findings indicate that at the levels of overall amino acid sequence identity and gene content, yeast shares a sister-group relationship with eubacteria, not with archaebacteria, in contrast to the current phylogenetic paradigm based on ribosomal RNA. Among eubacteria and archaebacteria, proteobacterial and methanogen genomes, respectively, shared more similarity with the yeast genome than other prokaryotic genomes surveyed