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An extensible ontology for inference of emergent whole cell function from relationships between subcellular processes

Whole cell responses arise from coordinated interactions between diverse human gene products functioning within various pathways underlying sub-cellular processes (SCP). Lower level SCPs interact to form higher level SCPs, often in a context specific manner to give rise to whole cell function. We sought to determine if capturing such relationships enables us to describe the emergence of whole cell functions from interacting SCPs. We developed the \"Molecular Biology of the Cell\" ontology based on standard cell biology and biochemistry textbooks and review articles. Currently, our ontology contains 5,392 genes, 753 SCPs and 19,182 expertly curated gene-SCP associations. Our algorithm to populate the SCPs with genes enables extension of the ontology on demand and the adaption of the ontology to the continuously growing cell biological knowledge. Since whole cell responses most often arise from the coordinated activity of multiple SCPs, we developed a dynamic enrichment algorithm that flexibly predicts SCP-SCP relationships beyond the current taxonomy. This algorithm enables us to identify interactions between SCPs as a basis for higher order function in a context dependent manner, allowing us to provide a detailed description of how SCPs together can give rise to whole cell functions. We conclude that this ontology can, from omics data sets, enable the development of detailed multidimensional SCP networks for predictive modeling of emergent whole cell functions.

systems biology↗

Two-Step Interphase Microtubule Disassembly Aids Spindle Morphogenesis

Entry into mitosis triggers profound changes in cell shape and cytoskeletal organisation. Here, by studying microtubule remodelling in human flat mitotic cells, we identify a two-step process of interphase microtubule disassembly. First, a microtubule stabilizing protein, Ensconsin, is inactivated in prophase as a consequence of its phosphorylation downstream of Cdk1/CyclinB. This leads to a reduction in interphase microtubule stability that may help to fuel the growth of centrosomally-nucleated microtubules. The peripheral interphase microtubules that remain are then rapidly lost as the concentration of tubulin heterodimers falls following dissolution of the nuclear compartment boundary. Finally, we show that a failure to destabilize microtubules in prophase leads to the formation of microtubule clumps, which interfere with spindle assembly. Overall, this analysis highlights the importance of the stepwise remodelling of the microtubule cytoskeleton, and the significance of permeabilization of the nuclear envelope in coordinating the changes in cellular organisation and biochemistry that accompany mitotic entry.

cell biology↗

Auxin Response Factors -- output control in auxin biology

The phytohormone auxin is involved in almost all developmental processes in land plants. Most, if not all, of these processes are mediated by changes in gene expression. Auxin acts on gene expression through a short nuclear pathway that converges upon the activation of a family of DNA-binding transcription factors. These AUXIN RESPONSE FACTORS (ARFs) are thus the effector of auxin response and translate the chemical signal to the regulation of a defined set of genes. Given the limited number of dedicated components in auxin signaling, distinct properties among the ARF family likely contributes to the establishment of multiple unique auxin responses in plant development. In the two decades following the identification of the first ARF in Arabidopsis much has been learnt about how these transcription factors act, and how they generate unique auxin responses. Progress in genetics, biochemistry, genomics and structural biology have helped to develop mechanistic models for ARF action. However, despite intensive efforts, many central questions are yet to be addressed. In this review we highlight what has been learnt about ARF transcription factors, and identify outstanding questions and challenges for the near future.

plant biology↗

Automated Recommendation Of Metabolite Substructures From Mass Spectra Using Frequent Pattern Mining

Despite the increasing importance of non-targeted metabolomics to answer various life science questions, extracting biochemically relevant information from metabolomics spectral data is still an incompletely solved problem. Most computational tools to identify tandem mass spectra focus on a limited set of molecules of interest. However, such tools are typically constrained by the availability of reference spectra or molecular databases, limiting their applicability to identify unknown metabolites. In contrast, recent advances in the field illustrate the possibility to expose the underlying biochemistry without relying on metabolite identification, in particular via substructure prediction. We describe an automated method for substructure recommendation motivated by association rule mining. Our framework captures potential relationships between spectral features and substructures learned from public spectral libraries. These associations are used to recommend substructures for any unknown mass spectrum. Our method does not require any predefined metabolite candidates, and therefore it can be used for the partial identification of unknown unknowns. The method is called MESSAR (MEtabolite SubStructure Auto-Recommender) and is implemented in a free online web service available at messar.biodatamining.be.\n\nAuthor SummaryMass spectrometry is one of most used techniques to detect and identify metabolites. However, learning metabolite structures directly from mass spectrometry data has always been a challenging task. Thousands of mass spectra from various biological systems still remain unanalyzed simply because no current bioinformatic tools are able to generate structural hypotheses. By manually studying mass spectra of standard compounds, chemists discovered that metabolites that share common substructures can also share spectral features. As data scientists, we believe that such relationships can be unraveled from massive structure and spectra data by machine learning. In this study, we adapted \"association rule mining\", traditionally used in market basket analysis, to structural and spectral data, allowing us to investigate all spectral features - metabolite substructures relationships. We further collected all statistically sound relationships into a database and used them to assign substructral hypotheses to unexplored spectra. We named our approach MESSAR, MEtabolite SubStructure Auto-Recommender, available to the metabolomics and mass spectrometry community as a free and open web service.

bioinformatics↗

Principles that govern competition or co-existence in Rho-GTPase driven polarization

Rho-GTPases are master regulators of polarity establishment and cell morphology. Positive feedback enables concentration of Rho-GTPases into clusters at the cell cortex, from where they regulate the cytoskeleton. Different cell types reproducibly generate either one (e.g. the front of a migrating cell) or several clusters (e.g. the multiple dendrites of a neuron), but the mechanistic basis for uni-polar or multi-polar outcomes is unclear. The design principles of Rho-GTPase circuits are captured by reaction-diffusion models based on conserved aspects of Rho-GTPase biochemistry. Some such models display rapid winner-takes-all competition between clusters, yielding a unipolar outcome. Other models allow prolonged co-existence of clusters. We derive a \"saturation rule\" general to all relevant models that governs the timescale of competition, and thereby predicts whether the system will generate uni-polar or multi-polar outcomes. We suggest that the saturation rule is a fundamental property of the Rho-GTPase polarity machinery, regardless of the specific feedback mechanism.

cell biology↗

Simple, single-step, and scar-free mutagenesis of bacterial genes

The need for generating precisely designed mutations is common in genetics, biochemistry, and molecular biology. Here, I describe a new {lambda} Red recombineering method (Direct and Inverted Repeat stimulated excision; DIRex) for fast and easy generation of single point mutations, small insertions or replacements as well as deletions of any size, in bacterial genes. The method does not leave any resistance marker or scar sequence and requires only one transformation to generate a semi-stable intermediate insertion mutant. Spontaneous excision of the intermediate efficiently and accurately generates the final mutant. In addition, the intermediate is transferable between strains by generalized transductions, enabling transfer of the mutation into multiple strains without repeating the recombineering step. Existing methods that can be used to accomplish similar results are either (i) more complicated to design, (ii) more limited in what mutation types can be made, or (iii) require expression of extrinsic factors in addition to {lambda} Red. I demonstrate the utility of the method by generating several deletions, small insertions/replacements, and single nucleotide exchanges in Escherichia coli and Salmonella enterica. Furthermore, the design parameters that influence the excision frequency and the success rate of generating desired point mutations have been examined to determine design guidelines for optimal efficiency.

synthetic biology↗

Lis1 has two opposing modes of regulating cytoplasmic dynein

Regulation is central to the functional versatility of cytoplasmic dynein, a motor involved in intracellular transport, cell division, and neurodevelopment. Previous work established that Lis1, a conserved and ubiquitous regulator of dynein, binds to its motor domain and induces a tight microtubule-binding state in dynein. The work we present here--a combination of biochemistry, single-molecule assays, cryo-electron microscopy and in vivo experiments--led to the surprising discovery that Lis1 has two opposing modes of regulating dynein, being capable of inducing both low and high affinity for the microtubule. We show that these opposing modes depend on the stoichiometry of Lis1 binding to dynein and that this stoichiometry is regulated by the nucleotide state of dyneins AAA3 domain. We present data on the in vitro and in vivo consequences of abolishing the novel Lis1-induced weak microtubule-binding state in dynein and propose a new model for the regulation of dynein by Lis1.

cell biology↗

ATP sensing in living plant cells reveals tissue gradients and stress dynamics of energy physiology

Growth and development of plants is ultimately driven by light energy captured through photosynthesis. ATP acts as universal cellular energy cofactor fuelling all life processes, including gene expression, metabolism, and transport. Despite a mechanistic understanding of ATP biochemistry, ATP dynamics in the living plant have been largely elusive. Here we establish live MgATP2- assessment in plants using the fluorescent protein biosensor ATeam1.03-nD/nA. We generate Arabidopsis sensor lines and investigate the sensor in vitro under conditions appropriate for the plant cytosol. We establish an assay for ATP fluxes in isolated mitochondria, and demonstrate that the sensor responds rapidly and reliably to MgATP2- changes in planta. A MgATP2- map of the Arabidopsis seedling highlights different MgATP2- concentrations between tissues and in individual cell types, such as root hairs. Progression of hypoxia reveals substantial plasticity of ATP homeostasis in seedlings, demonstrating that ATP dynamics can be monitored in the living plant.\n\nOne-sentence SummarySensing of MgATP2- by fluorimetry and microscopy allows dissection of ATP fluxes of isolated organelles, and dynamics of cytosolic MgATP2- in vivo.\n\nFunding AgenciesThis work was supported by the Deutsche Forschungsgemeinschaft (DFG) through the Emmy-Noether programme (SCHW1719/1-1; M.S. and GR4251/1-1; C.G.), the Research Training Group GRK 2064 (M.S.; A.J.M.), the Priority Program SPP1710 (A.J.M.) and a grant (SCHW1719/5-1; M.S.) as part of the package PAK918. The Seed Fund grant CoSens from the Bioeconomy Science Center, NRW (A.J.M.; M.S.) is gratefully acknowledged. The scientific activities of the Bioeconomy Science Center were financially supported by the Ministry of Innovation, Science and Research within the framework of the NRW Strategieprojekt BioSC (No. 313/323-400-002 13). A.Co. received funding by the Ministero dellIstruzione, dellUniversita e della Ricerca through the FIRB 2010 programme (RBFR10S1LJ_001) and Piano di Sviluppo di Ateneo 2015 (Universita degli Studi di Milano). M.Z. received funding by the Ministero dellIstruzione, dellUniversita e della Ricerca (Italy) through the PRIN 2010 programme (PRIN2010CSJX4F). S.W. and T.N. received travel support by the Deutscher Akademischer Austauschdienst (DAAD). V.D.C. was supported by the European Social Fund, Operational Programme 2007/2013, and an Erasmus+ Traineeship grant. M.D.F was supported by The Human Frontier Science Program (RPG0053/2012), and the Leverhulme Foundation (RPG-2015-437). I.M.M. was supported by a grant from the Danish Council for Independent Research - Natural Sciences. V.C.P. was supported by the Innovation and Technology Fund (Funding Support to Partner State Key Laboratories in Hong Kong) of the HKSAR.\n\nAbbreviationsAAC - ADP/ATP carrier; AK - adenylate kinase; cAT - carboxyatractyloside; CCCP - carbonyl cyanide m-chlorophenyl hydrazone; CFP - cyan fluorescent protein; CLSM - confocal laser scanning microscopy; ETC - electron transport chain; FRET - Forster Resonance Energy Transfer; LSFM - light sheet fluorescence microscopy.

plant biology↗

Data Resource Profile: Generation Scotland Electronic Health Record

This paper provides the first detailed demonstration of the research value of the Electronic Health Record (EHR) linked to research data in Generation Scotland Scottish Family Health Study (GS:SFHS) participants, together with how to access this data. The structured, coded variables in the routine biochemistry, prescribing and morbidity records in particular represent highly valuable phenotypic data for a genomics research resource. Access to a wealth of other specialized datasets including cancer, mental health and maternity inpatient information is also possible through the same straightforward and transparent application process. The Electronic Health Record linked dataset is a key component of GS:SFHS, a biobank conceived in 1999 for the purpose of studying the genetics of health areas of current and projected public health importance. Over 24,000 adults were recruited from 2006 to 2011, with broad and enduring written informed consent for biomedical research. Consent was obtained from 23,603 participants for GS:SFHS study data to be linked to their Scottish National Health Service (NHS) records, using their Community Health Index (CHI) number. This identifying number is used for NHS Scotland procedures (registrations, attendances, samples, prescribing and investigations) and allows healthcare records for individuals to be linked across time and location. Here, we describe the NHS EHR dataset on the sub-cohort of 20,032 GS:SFHS participants with consent and mechanism for record linkage plus extensive genetic data. Together with existing study phenotypes, including family history and environmental exposures such as smoking, the EHR is a rich resource of real world data that can be used in research to characterise the health trajectory of participants, available at low cost and a high degree of timeliness, matched to DNA, urine and serum samples and genome-wide genetic information.

genetics↗

Efficient hydrogen-dependent carbon dioxide reduction by Escherichia coli

The formate hydrogenlyase (FHL) complex of Escherichia coli is normally produced under anaerobic fermentative conditions when its physiological role is to oxidise formate to carbon dioxide and couple that reaction directly to the reduction of protons to molecular hydrogen. This forward reaction is the major route of hydrogen production by E. coli and the physiology, genetics and biochemistry of this process are reasonably well understood. However, studies of the reverse reaction - hydrogen-dependent carbon dioxide reduction - have been rather less extensive. Harnessing the alternative reverse reaction has the potential to unlock FHL as a carbon dioxide cycling enzyme, or could potentially lead to the development of bio-based carbon capture technologies. In this work, it is established that FHL can operate as a highly efficient CO2 reductase. A controllable pressure system was designed with the intention of maximising substrate availability to the FHL enzyme. By placing gaseous CO2 and H2 are under pressure (up to 10 bar), and by using a compartmentalised intact whole cell approach where the produced formate is excreted, the optimised experimental system was observed to convert 100 % of gaseous CO2 to formic acid and generate >500 mM formate in solution at an initial rate of 1.2 g formate per litre per hour.

microbiology↗

Spot-On: robust model-based analysis of single-particle tracking experiments

Single-particle tracking (SPT) has become an important method to bridge biochemistry and cell biology since it allows direct observation of protein binding and diffusion dynamics in live cells. However, accurately inferring information from SPT studies is challenging due to biases in both data analysis and experimental design. To address analysis bias, we introduce \"Spot-On\", an intuitive web-interface. Spot-On implements a kinetic modeling framework that accounts for known biases, including molecules moving out-of-focus, and robustly infers diffusion constants and subpopulations from pooled single-molecule trajectories. To minimize inherent experimental biases, we implement and validate stroboscopic photo-activation SPT (spaSPT), which minimizes motion-blur bias and tracking errors. We validate Spot-On using experimentally realistic simulations and show that Spot-On outperforms other methods. We then apply Spot-On to spaSPT data from live mammalian cells spanning a wide range of nuclear dynamics and demonstrate that Spot-On consistently and robustly infers subpopulation fractions and diffusion constants.\n\nIMPACT STATEMENTSpot-On is an easy-to-use website that makes a rigorous and bias-corrected modeling framework for analysis of single-molecule tracking experiments available to all.

biophysics↗

The effect of Wnt signaling on the localization, molecular size and activity of the beta-catenin destruction complex in vivo

Wnt signaling provides a paradigm for cell-cell signals that regulate embryonic development and stem cell homeostasis and are inappropriately activated in cancers. Our current outline of Wnt signaling focuses around several key players. The tumor suppressors APC and Axin form the core of the multiprotein destruction complex, which targets the Wnt-effector beta-catenin for phosphorylation, ubiquitination and destruction. However, mechanisms underlying destruction complex function and those by which Wnt signaling inactivates it remain much less clear. Based on work in cultured cells, we hypothesize the destruction complex is a supermolecular entity that self-assembles by Axin and APC polymerization, and that regulating complex assembly and dynamics underlie function. We took these insights into the Drosophila embryonic epidermis, a premier model of Wnt signaling. Combining biochemistry, genetic tools to manipulate Axin and APC2 levels, advanced imaging and molecule counting, we defined destruction complex assembly, stoichiometry, and localization in vivo, and its downregulation in response to Wnt signaling. Our findings challenge and revise current models of destruction complex function. Endogenous Axin and APC2 proteins accumulate at roughly similar levels, countering the accepted dogma that Axin accumulates at much lower levels. By expressing Axin:GFP at near endogenous levels we found Axin assembles into large cytoplasmic complexes containing tens to hundreds of Axin proteins. Wnt signals trigger complex recruitment to the membrane, while diffuse cytoplasmic Axin levels increase, suggesting slowed assembly. Manipulating Axin or APC2 levels had no effect on destruction complex activity when Wnt signals were absent, but, surprisingly, had opposite effects on the destruction complex when Wnt signals were present. Elevating Axin made the complex resistant to inactivation, while elevating APC2 levels enhanced inactivation. Our data suggest both absolute levels and the ratio of these two core components affect destruction complex function, supporting models in which competition among Axin partners determines destruction complex activity.\n\nAuthor SummaryCell-cell communication is critical for cells to choose fates during embryonic development and often goes wrong in diseases like cancer. The Wnt cell signaling pathway provides a superb example. Mutations in negative regulators like the proteins APC and Axin take the brakes off cell proliferation and thus contribute to colon cancer. We study how APC, Axin and their protein partners keep cell signaling off, and how cell-to-cell Wnt signals reverse this. We use the fruit fly embryo, combining biochemical, and genetic tools with advanced microscopy. We found that APC2 and Axin proteins are present in cells in similar numbers, challenging the previous dogma. We further find that the ability of Wnt signaling to turn off this negative regulatory machine is influenced both by the levels of Axin and APC2 and by the ratio of their protein levels. We also visualize the active destruction complex in the animal, and count the number of Axin proteins in this complex. Finally, we find that Wnt signals have two effects on the destruction complex--recruiting it to the cells plasma membrane and reducing its ability to assemble. Based on this, we propose a new model for how this important signaling pathway is regulated.\n\nAbbreviations

developmental biology↗

Characterization of Azotobacter vinelandii and Kits for Its Synthetic Biology Applications

Azotobacter vinelandii, a Gram-negative aerobic bacterium with an intracellular anaerobic environment that maintains the oxygen-sensitive enzymatic cascades for nitrogen fixation, could be used to express oxygen-sensitive proteins. However, little is known about the properties of A. vinelandii for synthetic biology applications. We therefore first characterized and optimized the conditions for growing and screening BioBrick constructs in A. vinelandii in the presence of 2 antibiotics, ampicillin and chloramphenicol, and then developed two sets of BioBricks for regulated protein expression. The first kit used T7 RNA polymerase, whose expression is under the control of a nitrogen-repressible nifH promoter. The commonly used T7-dependent system in Escherichia coli can then be used in A. vinelandii. Because its intracellular anaerobic environment is favorable for processes such as magnetosome biogenesis, we attempted to migrate the biogenesis machineries from the magnetotactic bacterium Magnetospirillum gryphiswaldense to A. vinelandii. During this undertaking, another insertion kit construct was developed to allow protein conjugation onto magnetosomes. The kit consists of mamC, a gene encoding a transmembrane protein on magnetosomes, and multiple restriction sites downstream of mamC for fusing a gene of interest. This insertion kit allows the attachment of any desired protein onto the magnetosome membrane by fusing with the mamC protein. We demonstrated the function of this kit by fusing mamC to a GFP nanobody. This kit will facilitate the conjugation of any target protein onto magnetosomes for downstream applications in the future.\n\nFinancial DisclosureWe received sponsorship from the 2012-15 Teaching Development Grants Triennium, Faculty of Engineering and Biochemistry Program, School of Life Sciences, The Chinese University of Hong Kong. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.\n\nCompeting InterestsThe authors declare that no competing interests exist.\n\nEthics StatementN/A.\n\nData AvailabilityAll data are fully available without restriction.

synthetic biology↗

A molecular model of the mitochondrial genome segregation machinery in Trypanosoma brucei

In almost all eukaryotes mitochondria maintain their own genome. Despite the discovery more than 50 years ago still very little is known about how the genome is properly segregated during cell division. The protozoan parasite Trypanosoma brucei contains a single mitochondrion with a singular genome the kinetoplast DNA (kDNA). Electron microscopy studies revealed the tripartite attachment complex (TAC) to physically connect the kDNA to the basal body of the flagellum and to ensure proper segregation of the mitochondrial genome via the basal bodies movement, during cell cycle. Using super-resolution microscopy we precisely localize each of the currently known unique TAC components. We demonstrate that the TAC is assembled in a hierarchical order from the base of the flagellum towards the mitochondrial genome and that the assembly is not dependent on the kDNA itself. Based on biochemical analysis the TAC consists of several non-overlapping subcomplexes suggesting an overall size of the TAC exceeding 2.8 mDa. We furthermore demonstrate that the TAC has an impact on mitochondrial organelle positioning however is not required for proper organelle biogenesis or segregation.\n\nSignificance StatementMitochondrial genome replication and segregation are essential processes in most eukaryotic cells. While replication has been studied in some detail much less is known about the molecular machinery required distribute the replicated genomes. Using super-resolution microscopy in combination with molecular biology and biochemistry we show for the first time in which order the segregation machinery is assembled and that it is assembled de novo rather than in a semi conservative fashion in the single celled parasite Trypanosoma brucei. Furthermore, we demonstrate that the mitochondrial genome itself is not required for assembly to occur. It seems that the physical connection of the mitochondrial genome to cytoskeletal elements is a conserved feature in most eukaryotes, however the molecular components are highly diverse.\n\nAbbreviation

cell biology↗

Distributed and dynamic intracellular organization of extracellular information

Although cells respond specifically to environments, how environmental identity is encoded intracellularly is not understood. Here we study this organization of information in budding yeast by estimating the mutual information between environmental transitions and the dynamics of nuclear translocation for ten transcription factors. Our method of estimation is general, scalable, and based on decoding from single cells. The dynamics of the transcription factors are necessary to encode the highest amounts of extracellular information, and we show that information is transduced through two channels: generalists (Msn2/4, Tod6/Dot6, Maf1, and Sfp1) can encode the nature of multiple stresses but only if stress is high; specialists (Hog1, Yap1, and Mig1/2) encode one particular stress, but do so more quickly and for a wider range of magnitudes. Each transcription factor reports differently, and it is only their collective response that distinguishes between multiple environmental states. Changes in the dynamics of the localization of transcription factors thus constitute a precise, distributed internal representation of extracellular change, and we predict that such multi-dimensional representations are common in cellular decision-making.\n\nSignificance StatementTo thrive in diverse environments, cells must represent extracellular change intracellularly despite stochastic biochemistry. Here we introduce a quantitative framework for investigating the organization of information within a cell. Combining single-cell measurements of intracellular dynamics with a new, scalable methodology for estimating mutual information between time-series and a discrete input, we demonstrate that extracellular information is encoded in the dynamics of the nuclear localization of transcription factors and that information is lost with alternative static statistics. Any one transcription factor is usually insufficient, but the collective dynamics of multiple transcription factors can represent complex extracellular change. We therefore show that a cells internal representation of its environment can be both distributed across diverse proteins and dynamically encoded.

systems biology↗

Homologues of key circadian clock genes present in Verticillium dahliae do not direct circadian programs of development or mRNA abundance.

Many organisms harbour circadian clocks that promote their adaptation to the rhythmic environment. While a broad knowledge of the molecular mechanism of circadian clocks has been gained through the fungal model Neurospora crassa, little is known about circadian clocks in other fungi. N. crassa belongs to the same class as many important plant pathogens including the vascular wilt fungus Verticillium dahliae. We identified homologues of N. crassa clock proteins in V. dahliae, which showed high conservation in key protein domains. However, no evidence for an endogenous, free-running and entrainable rhythm was observed in the daily formation of conidia and microsclerotia. In N. crassa the frequency (frq) gene encodes a central clock protein expressed rhythmically and in response to light. In contrast, expression of Vdfrq is not light-regulated. Temporal gene expression profiling over 48 hours in constant darkness and temperature revealed no circadian expression of key clock genes. Furthermore, RNA-seq over a 24 h time-course revealed no robust oscillations of RNA in constant darkness. Comparison of gene expression between wild-type V. dahliae and a{Delta} Vdfrq mutant showed that genes involved in metabolism, transport and redox processes are mis-regulated in the absence of Vdfrq. In addition, Vd{Delta}frq mutants display growth defects and reduced pathogenicity in a strain dependent manner. Our data indicate that if a circadian clock exists in Verticillium, it is based on alternative mechanisms such as post-transcriptional interactions of VdFRQ and the WC proteins or the components of a FRQ-less oscillator. Alternatively, it could be that whilst the original functions of the clock proteins have been maintained, in this species the interactions that generate rhythmicity have been lost or are only triggered when specific environmental conditions are met. The presence of conserved clock genes in genomes should not be taken as definitive evidence of circadian function. Author summaryCircadian clocks are used by organisms to orchestrate the activity of cellular processes such that they occur at an optimal time of day. Research carried out in the filamentous fungus Neurospora crassa has revealed a huge amount of information about the components its circadian clock, its interactions with the environment and how it drives cellular biochemistry and physiology. Although homologues of the Neurospora clock genes are present in a number of fungi, functional clocks have been demonstrated in a just a handful. Importantly, a link between the circadian clock of the plant pathogen Botrytis cinerea and virulence has recently been reported. We report that another significant plant pathogen, Verticillium dahliae, contains well-conserved homologues of all key clock genes. We find that diurnal development of conidia and microsclerotia is not influenced by a circadian clock. Furthermore, in a constant environment we find no evidence of rhythmic transcript accumulation. However, deletion of the central clock component results in altered growth and reduced virulence. This led us to question the role of clock genes in Verticillium. We are forced to consider that in this species the interactions that generate rhythmicity have been lost, are generated purely via post-transcriptional modification of clock proteins, are only triggered when specific environmental conditions are met or never evolved.

microbiology↗

Identifying Core Operons in Metagenomic Data

An operon is a functional unit of DNA whose genes are co-transcribed on polycistronic mRNA, in a co-regulated fashion. Operons are a powerful mechanism of introducing functional complexity in bacteria, and are therefore of interest in microbial genetics, physiology, biochemistry, and evolution. Here we present a Pipeline for Operon Exploration in Metagenomes or POEM. At the heart of POEM lies the concept of a core operon, a functional unit enabled by a predicted operon in a metagenome. Using a series of benchmarks, we show the high accuracy of POEM, and demonstrate its use on a human gut metagenome sample. We conclude that POEM is a useful tool for analyzing metagenomes beyond the genomic level, and for identifying multi-gene functionalities and possible neofunctionalization in metagenomes. Availability: https://github.com/Rinoahu/POEM_py3k

bioinformatics↗

Content of xylose, trehalose and L-citrulline in cucumber fermentations and utilization of such compounds by certain lactobacilli

This research determined the concentration of trehalose, xylose and L-citrulline in fresh and fermented cucumbers and their utilization by Lactobacillus pentosus, Lactobacillus plantarum, Lactobacillus brevis and Lactobacillus buchneri. Targeted compounds were measured by HPLC and the ability of certain lactobacilli to utilize them was scrutinized in fermented cucumber juice. Fresh cucumber juice was supplemented with trehalose, xylose and L-citrulline to observed mixed culture fermentations. Changes in the biochemistry, pH and colony counts during fermentations were monitored. Trehalose was detected in fermentations to 15.51 {+/-} 1.68 mM. Xylose was found in a fresh cucumber sample to 36.05 mM. L-citrulline was present in fresh and fermented cucumber samples to 1.05 {+/-} 0.63 mM. Most of the lactobacilli tested utilized trehalose and xylose in FCJM at pH 4.7. L-citrulline was utilized by L. buchneri and produced by other LAB. L-citrulline (12.43 {+/-} 2.3 mM) was converted to ammonia (14.54 {+/-} 3.60 mM) and the biogenic amine ornithine (14.19 {+/-} 1.07 mM) by L. buchneri at pH 4.7 in the presence of 0.5 {+/-} 0.2 mM glucose enhancing growth by 0.5 log CFU/mL. The use of a mixed starter culture containing L. buchneri aided in the removal of L-citrulline and enhanced the fermentation stability. The utilization of L-citrulline by L. buchneri may be a cause of concern for the stability of cucumber fermentations at pH 3.7 or above. This study identifies the use of a tripartite starter culture as an enhancer of microbial stability for fermented cucumbers. ImportanceUtilization of trehalose, xylose and L-citrulline as energy sources by the indigenous cucumber microbiota was studied to determine if this was a cause for the spoilage of the fermented fruit. While the plant derived sugars, trehalose and xylose, were occasionally present in cucumber fermentations, they are readily utilized by the bacteria spearheading primary fermentation. L-citrulline, however, is an amino acid not naturally found in proteins, was detected in all the samples tested and was uniquely utilized by the spoilage associated bacterium, L. buchneri. Additionally, the bacteria involved in cucumber fermentation produced L-citrulline. It was observed that the use of L. pentosus, L. brevis and L. buchneri in a mixed starter culture aids in the removal of the alternate energy sources, including L-citrulline, and the generation of a stable cucumber fermentation for 55 days under anaerobiosis.

microbiology↗