scholarly journals Determination of the Core of a Minimal Bacterial Gene Set

2004 ◽  
Vol 68 (3) ◽  
pp. 518-537 ◽  
Author(s):  
Rosario Gil ◽  
Francisco J. Silva ◽  
Juli Peretó ◽  
Andrés Moya
Keyword(s):  
Reduction Process ◽  
Minimal Cell ◽  
Bacterial Genomes ◽  
Protein Coding ◽  
Bacterial Gene ◽  
Gene Set ◽  
The Core ◽  
Metabolic Functions ◽  
Full Complement ◽  
Experimental Approaches

SUMMARY The availability of a large number of complete genome sequences raises the question of how many genes are essential for cellular life. Trying to reconstruct the core of the protein-coding gene set for a hypothetical minimal bacterial cell, we have performed a computational comparative analysis of eight bacterial genomes. Six of the analyzed genomes are very small due to a dramatic genome size reduction process, while the other two, corresponding to free-living relatives, are larger. The available data from several systematic experimental approaches to define all the essential genes in some completely sequenced bacterial genomes were also considered, and a reconstruction of a minimal metabolic machinery necessary to sustain life was carried out. The proposed minimal genome contains 206 protein-coding genes with all the genetic information necessary for self-maintenance and reproduction in the presence of a full complement of essential nutrients and in the absence of environmental stress. The main features of such a minimal gene set, as well as the metabolic functions that must be present in the hypothetical minimal cell, are discussed.

scholarly journals Minimal gene set from Sinorhizobium (Ensifer) meliloti pSymA required for efficient symbiosis with Medicago

2020 ◽  
Vol 118 (2) ◽  
pp. e2018015118
Author(s):  
Barney A. Geddes ◽  
Jason V. S. Kearsley ◽  
Jiarui Huang ◽  
Maryam Zamani ◽  
Zahed Muhammed ◽  
...  
Keyword(s):  
Root Nodules ◽  
Nodule Development ◽  
Nodule Formation ◽  
Protein Coding ◽  
Bacterial Gene ◽  
Gene Set ◽  
Background Strain ◽  
Genetic Components ◽  
Sustainable Agricultural Systems ◽  
Bacterial Genes

Reduction of N2 gas to ammonia in legume root nodules is a key component of sustainable agricultural systems. Root nodules are the result of a symbiosis between leguminous plants and bacteria called rhizobia. Both symbiotic partners play active roles in establishing successful symbiosis and nitrogen fixation: while root nodule development is mostly controlled by the plant, the rhizobia induce nodule formation, invade, and perform N2 fixation once inside the plant cells. Many bacterial genes involved in the rhizobia–legume symbiosis are known, and there is much interest in engineering the symbiosis to include major nonlegume crops such as corn, wheat, and rice. We sought to identify and combine a minimal bacterial gene complement necessary and sufficient for symbiosis. We analyzed a model rhizobium, Sinorhizobium (Ensifer) meliloti, using a background strain in which the 1.35-Mb symbiotic megaplasmid pSymA was removed. Three regions representing 162 kb of pSymA were sufficient to recover a complete N2-fixing symbiosis with alfalfa, and a targeted assembly of this gene complement achieved high levels of symbiotic N2 fixation. The resulting gene set contained just 58 of 1,290 pSymA protein-coding genes. To generate a platform for future synthetic manipulation, the minimal symbiotic genes were reorganized into three discrete nod, nif, and fix modules. These constructs will facilitate directed studies toward expanding the symbiosis to other plant partners. They also enable forward-type approaches to identifying genetic components that may not be essential for symbiosis, but which modulate the rhizobium’s competitiveness for nodulation and the effectiveness of particular rhizobia–plant symbioses.

scholarly journals Structural analyses of a hypothetical minimal metabolism

2007 ◽  
Vol 362 (1486) ◽  
pp. 1751-1762 ◽  
Author(s):  
Toni Gabaldón ◽  
Juli Peretó ◽  
Francisco Montero ◽  
Rosario Gil ◽  
Amparo Latorre ◽  
...  
Keyword(s):  
Large Scale ◽  
Minimal Cell ◽  
Bacterial Genomes ◽  
Protein Coding ◽  
Topological Parameters ◽  
Theoretical Design ◽  
Significant Damage ◽  
Complex Power ◽  
Computational Analyses ◽  
Steady State Solutions

By integrating data from comparative genomics and large-scale deletion studies, we previously proposed a minimal gene set comprising 206 protein-coding genes. To evaluate the consistency of the metabolism encoded by such a minimal genome, we have carried out a series of computational analyses. Firstly, the topology of the minimal metabolism was compared with that of the reconstructed networks from natural bacterial genomes. Secondly, the robustness of the metabolic network was evaluated by simulated mutagenesis and, finally, the stoichiometric consistency was assessed by automatically deriving the steady-state solutions from the reaction set. The results indicated that the proposed minimal metabolism presents stoichiometric consistency and that it is organized as a complex power-law network with topological parameters falling within the expected range for a natural metabolism of its size. The robustness analyses revealed that most random mutations do not alter the topology of the network significantly, but do cause significant damage by preventing the synthesis of several compounds or compromising the stoichiometric consistency of the metabolism. The implications that these results have on the origins of metabolic complexity and the theoretical design of an artificial minimal cell are discussed.

Serial Homology as a Challenge to Evolutionary Theory

2017 ◽  
Author(s):  
Stéphane Schmitt
Keyword(s):  
Biological Sciences ◽  
Evolutionary Theory ◽  
Serial Homology ◽  
The Core ◽  
Long Period ◽  
Colonial Theory ◽  
Experimental Approaches ◽  
Evo Devo ◽  
The 19Th Century ◽  
Development And Evolution

The problem of the repeated parts of organisms was at the center of the biological sciences as early as the first decades of the 19th century. Some concepts and theories (e.g., serial homology, unity of plan, or colonial theory) introduced in order to explain the similarity as well as the differences between the repeated structures of an organism were reused throughout the 19th and the 20th century, in spite of the fundamental changes during this long period that saw the diffusion of the evolutionary theory, the rise of experimental approaches, and the emergence of new fields and disciplines. Interestingly, this conceptual heritage was at the core of any attempt to unify the problems of inheritance, development, and evolution, in particular in the last decades, with the rise of “evo-devo.” This chapter examines the conditions of this theoretical continuity and the challenges it brings out for the current evolutionary sciences.

scholarly journals Sequencing of Organellar Genomes of Nowellia curvifolia (Cephaloziaceae Jungermanniales) Revealed the Smallest Plastome with Complete Gene Set and High Intraspecific Variation Suggesting Cryptic Speciation

Diversity ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 81
Author(s):  
Jakub Sawicki ◽  
Katarzyna Krawczyk ◽  
Monika Ślipiko ◽  
Monika Szczecińska
Keyword(s):  
Cryptic Speciation ◽  
Editing Event ◽  
Protein Coding ◽  
Gene Set ◽  
Protein Coding Genes ◽  
Organellar Genomes ◽  
The Family ◽  
Leafy Liverwort ◽  
Aneura Mirabilis ◽  
First Time

The leafy liverwort Nowellia curvifolia is a widespread Holarctic species belonging to the family Cephaloziaceae. It is made up of a newly sequenced, assembled and annotated organellar genomes of two European specimens, which revealed the structure typical for liverworts, but also provided new insights into its microevolution. The plastome of N. curvifolia is the second smallest among photosynthetic liverworts, with the shortest known inverted repeats. Moreover, it is the smallest liverwort genome with a complete gene set, since two smaller genomes of Aneura mirabilis and Cololejeunea lanciloba are missing six and four protein-coding genes respectively. The reduction of plastome size in leafy liverworts seems to be mainly impacted by deletion within specific region between psbA and psbD genes. The comparative intraspecific analysis revealed single SNPs difference among European individuals and a low number of 35 mutations differentiating European and North American specimens. However, the genetic resources of Asian specimen enabled to identify 1335 SNPs in plastic protein-coding genes suggesting an advanced cryptic speciation within N. curvifolia or the presence of undescribed morphospecies in Asia. Newly sequenced mitogenomes from European specimens revealed identical gene content and structure to previously published and low intercontinental differentiation limited to one substitution and three indels. The RNA-seq based RNA editing analysis revealed 17 and 127 edited sites in plastome and mitogenome respectively including one non-canonical editing event in plastid chiL gene. The U to C editing is common in non-seed plants, but in liverwort plastome is reported for the first time.

scholarly journals Fusarium verticillioides FvPex8 is a key component of peroxisomal docking/translocation module that serves important roles in fumonisin biosynthesis but not in virulence

2020 ◽  
Author(s):  
Wenying Yu ◽  
Mei Lin ◽  
Minghui Peng ◽  
Huijuan Yan ◽  
Jie Zhou ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Fusarium Verticillioides ◽  
Fumonisin B1 ◽  
Gene Expression Profiles ◽  
Deletion Mutants ◽  
Altered Expression ◽  
The Core ◽  
Metabolic Functions ◽  
Peroxisome Membrane

AbstractPeroxisomes are ubiquitous organelles in eukaryotic cells that fulfill various important metabolic functions. In this study, we investigated the role of Docking/Translocation Module (DTM) peroxins, mainly FvPex8, FvPex13, FvPex14, and FvPex33, in Fusarium verticillioides virulence and fumonisin B1 (FB1) biosynthesis. Protein interaction experiments suggested that FvPex13 serves as the core subunit of F. verticillioides DTM. When we generated gene deletion mutants (ΔFvpex8, ΔFvpex13, ΔFvpex14, ΔFvpex33, ΔFvpex33/14) and examined whether the expression of other peroxin genes were affected in the DTM mutants, ΔFvpex8 strain showed most drastic changes to PEX gene expression profiles. Deletion mutants exhibited disparity in carbon source utilization and defect in cell wall integrity when stress agents were applied. Under nutrient starvation, mutants also showed higher levels of lipid droplet accumulation. Notably, ΔFvpex8 mutant showed significant FB1 reduction and altered expression of FUM1 and FUM19 genes. However, FvPex13 was primarily responsible for virulence, while ΔFvpex33/14 double mutant also showed virulence defect. In summary, our study suggests that FvPex13 is the core component of DTM, regulating peroxisome membrane biogenesis as well as PTS1- and PTS2-mediated transmembrane cargo transportation. Importantly, we predict FvPex8 as a key component in DTM that affects peroxisome function in FB1 biosynthesis in F. verticillioides.

scholarly journals Identification and characterization of cis-regulatory elements for photoreceptor type-specific transcription in zebrafish

2019 ◽  
Author(s):  
Wei Fang ◽  
Yi Wen ◽  
Xiangyun Wei
Keyword(s):  
Core Promoter ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Protein Coding ◽  
Core Promoters ◽  
Protein Coding Genes ◽  
The Core ◽  
Cell Type Specific ◽  
Identification And Characterization

AbstractTissue-specific or cell type-specific transcription of protein-coding genes is controlled by both trans-regulatory elements (TREs) and cis-regulatory elements (CREs). However, it is challenging to identify TREs and CREs, which are unknown for most genes. Here, we describe a protocol for identifying two types of transcription-activating CREs—core promoters and enhancers—of zebrafish photoreceptor type-specific genes. This protocol is composed of three phases: bioinformatic prediction, experimental validation, and characterization of the CREs. To better illustrate the principles and logic of this protocol, we exemplify it with the discovery of the core promoter and enhancer of the mpp5b apical polarity gene (also known as ponli), whose red, green, and blue (RGB) cone-specific transcription requires its enhancer, a member of the rainbow enhancer family. While exemplified with an RGB cone-specific gene, this protocol is general and can be used to identify the core promoters and enhancers of other protein-coding genes.

scholarly journals Neuromolecular Underpinnings of Negative Cognitive Bias in Depression

Cells ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 3157
Author(s):  
Karolina Noworyta ◽  
Agata Cieslik ◽  
Rafal Rygula
Keyword(s):  
Cognitive Function ◽  
Depressive Disorder ◽  
Cognitive Bias ◽  
Judgment Bias ◽  
Cognitive Correlates ◽  
The Core ◽  
Pharmacological Challenge ◽  
Treatment Of Depression ◽  
Abnormal Response ◽  
Experimental Approaches

This selective review aims to summarize the recent advances in understanding the neuromolecular underpinnings of biased cognition in depressive disorder. We begin by considering the cognitive correlates of depressed mood and the key brain systems implicated in its development. We then review the core findings across two domains of biased cognitive function in depression: pessimistic judgment bias and abnormal response to negative feedback. In considering their underlying substrates, we focus on the neurochemical mechanisms identified by genetic, molecular and pharmacological challenge studies. We conclude by discussing experimental approaches to the treatment of depression, which are derived largely from an improved understanding of its cognitive substrates.

Deep learning with evolutionary and genomic profiles for identifying cancer subtypes

2019 ◽  
Vol 17 (03) ◽  
pp. 1940005 ◽  
Author(s):  
Chun-Yu Lin ◽  
Peiying Ruan ◽  
Ruiming Li ◽  
Jinn-Moon Yang ◽  
Simon See ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Deep Learning ◽  
Evolutionary Conservation ◽  
Core Gene ◽  
Breast Cancer Subtypes ◽  
Gene Set ◽  
Cancer Subtypes ◽  
The Core ◽  
Cancer Types ◽  
Core Genes

Cancer subtype identification is an unmet need in precision diagnosis. Recently, evolutionary conservation has been indicated to contain informative signatures for functional significance in cancers. However, the importance of evolutionary conservation in distinguishing cancer subtypes remains largely unclear. Here, we identified the evolutionarily conserved genes (i.e. core genes) and observed that they are primarily involved in cellular pathways relevant to cell growth and metabolisms. By using these core genes, we developed two novel strategies, namely a feature-based strategy (FES) and an image-based strategy (IMS) by integrating their evolutionary and genomic profiles with the deep learning algorithm. In comparison with the FES using the random set and the strategy using the PAM50 classifier, the core gene set-based FES achieved a higher accuracy for identifying breast cancer subtypes. The IMS and FES using the core gene set yielded better performances than the other strategies, in terms of classifying both breast cancer subtypes and multiple cancer types. Moreover, the IMS is reproducible even using different gene expression data (i.e. RNA-seq and microarray). Comprehensive analysis of eight cancer types demonstrates that our evolutionary conservation-based models represent a valid and helpful approach for identifying cancer subtypes and the core gene set offers distinguishable clues of cancer subtypes.

scholarly journals Identification of a transposable genomic island of Paracoccus pantotrophus DSM 11072 by its transposition to a novel entrapment vector pMMB2

Microbiology ◽  
2006 ◽  
Vol 152 (4) ◽  
pp. 1063-1073 ◽  
Author(s):  
Malgorzata Mikosa ◽  
Marta Sochacka-Pietal ◽  
Jadwiga Baj ◽  
Dariusz Bartosik
Keyword(s):  
Genomic Island ◽  
Tricarboxylic Acid Cycle ◽  
Housekeeping Genes ◽  
Core Region ◽  
Lateral Transfer ◽  
Large Set ◽  
Bacterial Genomes ◽  
The Core ◽  
Chromosomal Origin ◽  
Paracoccus Pantotrophus

A novel shuttle entrapment vector, pMMB2, was used to identify a large transposable element, TnPpa1 (44·3 kb), of Paracoccus pantotrophus DSM 11072. TnPpa1 has a composite structure with divergently oriented copies of a cryptic transposon, Tn3434 (Tn3 family), located at both termini. The core region of the element contains a large set of putative genes, whose products show similarity to enzymes involved in central intermediary metabolism (e.g. tricarboxylic acid cycle or 2-methylcitrate cycle), transporters, transcriptional regulators and conserved proteins of unknown function. A 4·2 kb DNA segment of TnPpa1 is homologous to a region of chromosome cII of Rhodobacter sphaeroides 2.4.1, which exemplifies the mosaic structure of this element. TnPpa1 is bordered by 5 bp long directly repeated sequences and is located within a mega-sized replicon, pWKS5, in the DSM 11072 genome. Spontaneous inversion of the core region of TnPpa1 was detected in the host genome. Analysis of the distribution of TnPpa1 in three other strains of P. pantotrophus revealed that this element was present exclusively within DSM 11072, which suggests its relatively recent acquisition by lateral transfer. The identification of TnPpa1 (which may be considered a transposable genomic island) provides evidence for the transposition and lateral transfer of large DNA segments of chromosomal origin (carrying various housekeeping genes), which may have a great impact on the evolution of bacterial genomes.

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