Joana C. Xavier

Joana C. Xavier
University College London | UCL

PhD in Chemical and Biological Engineering

About

47
Publications
13,530
Reads
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834
Citations
Citations since 2016
46 Research Items
831 Citations
2016201720182019202020212022050100150200250
2016201720182019202020212022050100150200250
2016201720182019202020212022050100150200250
2016201720182019202020212022050100150200250
Introduction
Joana C. Xavier currently works at UCL, UK. Joana does research in molecular evolution, metabolic networks and the origin of prokaryotes.
Additional affiliations
March 2017 - October 2020
Heinrich-Heine-Universität Düsseldorf
Position
  • Researcher
March 2014 - June 2014
Argonne National Laboratory
Position
  • Visiting Scientist
January 2012 - May 2016
University of Minho
Position
  • PhD
Education
September 2006 - July 2011
University of Porto
Field of study
  • Bioengineering

Publications

Publications (47)
Article
Life and the genetic code are self-referential and so are autocatalytic networks made of simpler, small molecules. Several origins of life theories postulate autocatalytic chemical networks preceding the primordial genetic code, yet demonstration with biochemical systems is lacking. Here, small-molecule reflexively autocatalytic food-generated netw...
Article
A closer look at Wilhelm Ostwald's articles that originally proposed the concept of autocatalysis reveals that he accepted reactants, not just products, as potential autocatalysts. Therefore, that a process is catalyzed by some of its products, which is the common definition of autocatalysis, is only a proper subset of what Ostwald meant by “Autoka...
Article
Full-text available
Though all theories for the origin of life require a source of energy to promote primordial chemical reactions, the nature of energy that drove the emergence of metabolism at origins is still debated. We reasoned that evidence for the nature of energy at origins should be preserved in the biochemical reactions of life itself, whereby changes in fre...
Article
Full-text available
Bacteria are the most abundant cells on Earth. They are generally regarded as ancient, but due to striking diversity in their metabolic capacities and widespread lateral gene transfer, the physiology of the first bacteria is unknown. From 1089 reference genomes of bacterial anaerobes, we identified 146 protein families that trace to the last bacter...
Article
Full-text available
Bacteria are the most abundant cells on Earth. They are generally regarded as ancient, but due to striking diversity in their metabolic capacities and widespread lateral gene transfer, the physiology of the first bacteria is unknown. From 1089 reference genomes of bacterial anaerobes, we identified 146 protein families that trace to the last bacter...
Article
Full-text available
The last eukaryote common ancestor (LECA) possessed mitochondria and all key traits that make eukaryotic cells more complex than their prokaryotic ancestors, yet the timing of mitochondrial acquisition and the role of mitochondria in the origin of eukaryote complexity remain debated. Here we report evidence from gene duplications in LECA indicating...
Article
Full-text available
The metabolism of cells contains evidence reflecting the process by which they arose. Here, we have identified the ancient core of autotrophic metabolism encompassing 404 reactions that comprise the reaction network from H2, CO2, and ammonia (NH3) to amino acids, nucleic acid monomers, and the 19 cofactors required for their synthesis. Water is the...
Article
Full-text available
Metabolism across all known living systems combines two key features. First, all of the molecules that are required are either available in the environment or can be built up from available resources via other reactions within the system. Second, the reactions proceed in a fast and synchronized fashion via catalysts that are also produced within th...
Preprint
Full-text available
Metabolism across all known living systems combines two key features. First, all of the molecules that are required are either available in the environment or can be built up from available resources via other reactions within the system. Second, the reactions proceed in a fast and synchronised fashion via catalysts that are also produced within th...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
Full-text available
Modern cells embody metabolic networks containing thousands of elements and form autocatalytic sets of molecules that produce copies of themselves. How the first self-sustaining metabolic networks arose at life's origin is a major open question. Autocatalytic sets smaller than metabolic networks were proposed as transitory intermediates at the orig...
Article
Full-text available
Research on the origin of life is highly heterogeneous. After a peculiar historical development, it still includes strongly opposed views which potentially hinder progress. In the 1st Interdisciplinary Origin of Life Meeting, early-career researchers gathered to explore the commonalities between theories and approaches, critical divergence points,...
Article
The physical linkage of the first self-replicating molecules is likely to have been selected based on their capacity to perform cooperative catalysis.
Article
Full-text available
If life on Earth started out in geochemical environments like hydrothermal vents, then it started out from gasses like CO2, N2 and H2. Anaerobic autotrophs still live from these gasses today, and they still inhabit the Earth's crust. In the search for connections between abiotic processes in ancient geological systems and biotic processes in biolog...
Article
Full-text available
One contribution of 14 to a theme issue 'The origin of life: the submarine alkaline vent theory at 30'. If life on Earth started out in geochemical environments like hydrothermal vents, then it started out from gasses like CO2, N2, and H2. Anaerobic autotrophs still live from these gasses today, and they still inhabit the Earth's crust. In the sear...
Preprint
The last eukaryote common ancestor (LECA) lived 1.6 billion years ago. It possessed nuclei, sex, an endomembrane system, mitochondria, and all key traits that make eukaryotic cells more complex than their prokaryotic ancestors. The closest known relatives of the host lineage that acquired the mitochondrion are, however, small obligately symbiotic a...
Preprint
Full-text available
Modern cells embody metabolic networks containing thousands of elements and form autocatalytic molecule sets that produce copies of themselves. How the first self-sustaining metabolic networks arose at life's origin is a major open question. Autocatalytic molecule sets smaller than metabolic networks were proposed as transitory intermediates at the...
Article
Three recent metagenomic studies analyse methanogenesis-related genes in previously uncharacterized, sediment-inhabiting archaeal lineages. They elucidate the metabolic capacity encoded in the genomes of these lineages, yet how these organisms harness energy is still a mystery.
Article
Full-text available
Self-sustaining autocatalytic networks play a central role in living systems, from metabolism at the origin of life, simple RNA networks and the modern cell, to ecology and cognition. A collectively autocatalytic network that can be sustained from an ambient food set is also referred to more formally as a 'reflexively autocatalytic food-generated'...
Article
Full-text available
Essential metabolic reactions are shaping constituents of metabolic networks, enabling viable and distinct phenotypes across diverse life forms. Here we analyse and compare modelling predictions of essential metabolic functions with experimental data and thereby identify core metabolic pathways in prokaryotes. Simulations of 15 manually curated gen...
Data
Phylogenetic reference tree for species used in the analysis of conservation of essential genes (based on NCBI taxonomy). (PDF)
Data
Highly conserved cofactor biosynthesis genes in prokaryotic genomes. Essentiality is given as the number of datasets in DEG (out of 36) in which each gene is essential. Conservation is given as the percentage of the 79 genomes where a significant homolog for this gene was found. The description is that of the corresponding annotated ORF in the geno...
Data
Essential reactions in metabolic models. Presence-absence matrix of essential reactions in the 15 GSMs used. (XLSX)
Data
Essentiality and conservation scores. List of genes with corresponding scores of essentiality and conservation. (XLSX)
Data
COG functional categories for prokaryotic essential genes in DEG. COG metabolic functional categories are less detailed than those used in the annotation of metabolic models: both the “Energy production and Conversion” and “Amino acid transport and metabolism” functional categories encompass several of those that are detailed within GSMs, except fo...
Data
Ubiquitous transporter genes. The list includes genes conserved in all 79 prokaryotic genomes analysed. Essentiality is given as the number of datasets in DEG (out of 36) in which each gene is essential. The description is that of the corresponding annotated ORF in the genome of E. coli K12. (PDF)
Data
Translation of metabolic subsystems of GSMs to a standardized nomenclature. Lists of original subsystem classifications and corresponding translation for all models and all reactions. (XLSX)
Data
Fig. S1. CO2 in a global metabolic map. KEGG map ‘01100 – metabolic pathways’ with reactions involving CO2 highlighted, portraying different directionality and reversibility assignments in BRENDA.
Article
Full-text available
Background: The origin of eukaryotic cells was an important transition in evolution. The factors underlying the origin and evolutionary success of the eukaryote lineage are still discussed. One camp argues that mitochondria were essential for eukaryote origin because of the unique configuration of internalized bioenergetic membranes that they conf...
Article
Full-text available
Rock–water–carbon interactions germane to serpentinization in hydrothermal vents have occurred for over 4 billion years, ever since there was liquid water on Earth. Serpentinization converts iron(II) containing minerals and water to magnetite (Fe3O4) plus H2. The hydrogen can generate native metals such as awaruite (Ni3Fe), a common serpentinizatio...
Article
Full-text available
Carbon dioxide enters metabolism via six known CO2 fixation pathways, of which only one is linear, exergonic in the direction of CO2‐assimilation, and present in both bacterial and archaeal anaerobes – the Wood‐Ljungdahl (WL) or reductive acetyl‐CoA pathway. Carbon monoxide (CO) plays a central role in the WL pathway as an energy rich intermediate....
Article
Full-text available
All known life forms trace back to a last universal common ancestor (LUCA) that witnessed the onset of Darwinian evolution. One can ask questions about LUCA in various ways, the most common way being to look for traits that are common to all cells, like ribosomes or the genetic code. With the availability of genomes, we can, however, also ask what...
Data
ML trees for the 355 protein families that trace to LUCA by phylogenetic criteria. The trees are for the 355 clusters that, after alignment and tree construction, generated ML trees that preserve domain monophyly while also having homologues in ≥2 archaeal and ≥2 bacterial lineages. These 355 proteins trace to LUCA by those phylogenetic criteria [7...
Preprint
Full-text available
Several studies have shown that neither the formal representation nor the functional requirements of genome-scale metabolic models (GEMs) are precisely defined. Without a consistent standard, comparability, reproducibility, and interoperability of models across groups and software tools cannot be guaranteed. Here, we present memote ( https://github...
Article
Full-text available
In prokaryotes, known mechanisms of lateral gene transfer (transformation, transduction, conjugation, and gene transfer agents) generate new combinations of genes among chromosomes during evolution. In eukaryotes, whose host lineage is descended from archaea, lateral gene transfer from organelles to the nucleus occurs at endosymbiotic events. Recen...
Preprint
Full-text available
In prokaryotes, known mechanisms of lateral gene transfer (transformation, transduction, conjugation and gene transfer agents) generate new combinations of genes among chromosomes during evolution. In eukaryotes, whose host lineage is descended from archaea, lateral gene transfer from organelles to the nucleus occurs at endosymbiotic events. Recent...
Data
Supplementary material: Supplementary Datasets 7–9: Supplementary Datasets on BOF swaps.
Data
Supplementary material: Supplementary Datasets 18–19: Essentiality predictions by modified iNJ661v.
Data
Supplementary material: iNJ661v_modified : iNJ661v model in SBML format with Vitamin B6 biosynthesis, completed BOF with essential vitamins and biotin and pyridoxine transport.
Data
Supplementary material: Supplementary Information: Supplementary Discussion and References, Supplementary Table 1 and Supplementary Figure 1..
Data
Supplementary material: Supplementary Datasets 1–6: GSM collection and nomenclature mappings.
Data
Supplementary material: Supplementary Datasets 12–17: Supplementary Datasets on the Pipeline to Find Essential Cofactors.
Data
Supplementary material: Supplementary Datasets 10–11: Supplementary Datasets on Klebsiella pneumoniae new essentials and mapping with DEG.
Article
Full-text available
The composition of a cell in terms of macromolecular building blocks and other organic molecules underlies the metabolic needs and capabilities of a species. Although some core biomass components such as nucleic acids and proteins are evident for most species, the essentiality of the pool of other organic molecules, especially cofactors and prosthe...
Article
Full-text available
SUMMARY The concept of the minimal cell has fascinated scientists for a long time, from both fundamental and applied points of view. This broad concept encompasses extreme reductions of genomes, the last universal common ancestor (LUCA), the creation of semiartificial cells, and the design of protocells and chassis cells. Here we review these diffe...

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Project
http://dd-decaf.eu/