Integration of molecular functions at the ecosystemic level: breakthroughs and future goals of environmental genomics and post-genomics

Environmental genomics and genome-wide expression approaches deal with large-scale sequence-based information obtained from environmental samples, at organismal, population or community levels. To date, environmental genomics, transcriptomics and proteomics are arguably the most powerful approaches to discover completely novel ecological functions and to link organismal capabilities, organism–environment interactions, functional diversity, ecosystem processes, evolution and Earth history. Thus, environmental genomics is not merely a toolbox of new technologies but also a source of novel ecological concepts and hypotheses. By removing previous dichotomies between ecophysiology, population ecology, community ecology and ecosystem functioning, environmental genomics enables the integration of sequence-based information into higher ecological and evolutionary levels. However, environmental genomics, along with transcriptomics and proteomics, must involve pluridisciplinary research, such as new developments in bioinformatics, in order to integrate high-throughput molecular biology techniques into ecology. In this review, the validity of environmental genomics and post-genomics for studying ecosystem functioning is discussed in terms of major advances and expectations, as well as in terms of potential hurdles and limitations. Novel avenues for improving the use of these approaches to test theory-driven ecological hypotheses are also explored

Varieties of living things: Life at the intersection of lineage and metabolism

publication-status: Publishedtypes: Articl

Methylobacterium Genome Sequences: A Reference Blueprint to Investigate Microbial Metabolism of C1 Compounds from Natural and Industrial Sources

Methylotrophy describes the ability of organisms to grow on reduced organic compounds without carbon-carbon bonds. The genomes of two pink-pigmented facultative methylotrophic bacteria of the Alpha-proteobacterial genus Methylobacterium, the reference species Methylobacterium extorquens strain AM1 and the dichloromethane-degrading strain DM4, were compared. Methodology/Principal Findings The 6.88 Mb genome of strain AM1 comprises a 5.51 Mb chromosome, a 1.26 Mb megaplasmid and three plasmids, while the 6.12 Mb genome of strain DM4 features a 5.94 Mb chromosome and two plasmids. The chromosomes are highly syntenic and share a large majority of genes, while plasmids are mostly strain-specific, with the exception of a 130 kb region of the strain AM1 megaplasmid which is syntenic to a chromosomal region of strain DM4. Both genomes contain large sets of insertion elements, many of them strain-specific, suggesting an important potential for genomic plasticity. Most of the genomic determinants associated with methylotrophy are nearly identical, with two exceptions that illustrate the metabolic and genomic versatility of Methylobacterium. A 126 kb dichloromethane utilization (dcm) gene cluster is essential for the ability of strain DM4 to use DCM as the sole carbon and energy source for growth and is unique to strain DM4. The methylamine utilization (mau) gene cluster is only found in strain AM1, indicating that strain DM4 employs an alternative system for growth with methylamine. The dcm and mau clusters represent two of the chromosomal genomic islands (AM1: 28; DM4: 17) that were defined. The mau cluster is flanked by mobile elements, but the dcm cluster disrupts a gene annotated as chelatase and for which we propose the name “island integration determinant” (iid).Conclusion/Significance These two genome sequences provide a platform for intra- and interspecies genomic comparisons in the genus Methylobacterium, and for investigations of the adaptive mechanisms which allow bacterial lineages to acquire methylotrophic lifestyles.Organismic and Evolutionary Biolog

A paralog of a bacteriochlorophyll biosynthesis enzyme catalyzes the formation of 1,2-dihydro-carotenoids in green sulfur bacteria

Chlorobaculum tepidum, a green sulfur bacterium, utilizes chlorobactene as its major carotenoid, and this organism also accumulates a reduced form of this monocyclic pigment, 1',2'-dihydrochlorobactene. The protein catalyzing this reduction is the last unidentified enzyme in the biosynthetic pathways for all of the green sulfur bacterial pigments used for photosynthesis. The genome of Chlorobaculum tepidum contains two paralogous genes encoding members of the FixC family of flavoproteins: bchP, that has been shown to encode an enzyme of bacteriochlorophyll biosynthesis; and bchO, for which a function has not been assigned. Here we demonstrate that a bchO mutant is unable to synthesize 1',2'-dihydrochlorobactene, and when bchO is heterologously expressed in a neurosporene-producing mutant of the purple bacterium, Rhodobactersphaeroides, the encoded protein is able to catalyze the formation of 1,2-dihydroneurosporene, the major carotenoid of the only other organism reported to synthesize 1,2-dihydrocarotenoids, Blastochloris viridis Identification of this enzyme completes the pathways for the synthesis of photosynthetic pigments in Chlorobiaceae, and accordingly and consistent with its role in carotenoid biosynthesis, we propose to rename the gene, cruI Notably, the absence of cruI in Blastochloris viridis indicates that a second 1,2-carotenoid reductase, which is structurally unrelated to CruI (BchO), must exist in nature. The evolution of this carotenoid reductase in green sulfur bacteria is discussed herein

We're in this Together: Sensation of the Host Cell Environment by Endosymbiotic Bacteria

Bacteria inhabit diverse environments, including the inside of eukaryotic cells. While a bacterial invader may initially act as a parasite or pathogen, a subsequent mutualistic relationship can emerge in which the endosymbiotic bacteria and their host share metabolites. While the environment of the host cell provides improved stability when compared to an extracellular environment, the endosymbiont population must still cope with changing conditions, including variable nutrient concentrations, the host cell cycle, host developmental programs, and host genetic variation. Furthermore, the eukaryotic host can deploy mechanisms actively preventing a bacterial return to a pathogenic state. Many endosymbionts are likely to use two-component systems (TCSs) to sense their surroundings, and expanded genomic studies of endosymbionts should reveal how TCSs may promote bacterial integration with a host cell. We suggest that studying TCS maintenance or loss may be informative about the evolutionary pathway taken toward endosymbiosis, or even toward endosymbiont-to-organelle conversion.Peer reviewe

T cell receptors from the HIV-specific repertoire, means for their production and therapeutic uses thereof

The present invention pertains to the field of T Cell receptors (TCR) identification and clonotyping, and especially concerns particular TCRs identified by clonotyping of a HIV-specific TCR repertoire, or fragments thereof. the invention relates especially to TCRs recognizing Gag peptide located between positions 293-312 in the GAG protein of HIV-1. The present invention further relates to nucleic acid constructs suitable as means for cloning or expressing nucleic acid molecules or TCRs of the invention, such as plasmids, vectors, especially lentiviral transfer vectors. The invention is of particular interest in the context of therapeutic treatment of human beings seropositive for HIV

MHC Class II Tetramer Labeling of Human Primary CD4+ T Cells from HIV Infected Patients

Major Histocompatibility Complex (MHC) tetramers have been used for two decades to detect, isolate and characterize T cells specific for various pathogens and tumor antigens. In the context of Human Immunodeficiency Virus (HIV) infection, antigen-specific CD8+ T cells have been extensively studied ex vivo, as they can be readily detected by HIV peptide-loaded MHC class I tetramers. In contrast, the detection of HIV-specific CD4+ T cells has proven more challenging, due to the intrinsically lower clonal expansion rates of CD4+ T cells, and to the preferential depletion of HIV-specific CD4+ T cells in the course of HIV infection. In the following protocol, we describe a simple method that facilitates the identification of CD4+ T cells specific for an HIV-1 capsid epitope using peptide-loaded MHC class II tetramers. Tetramer labeled CD4+ T cells can be analyzed for their cell surface phenotype and/or FACS-sorted for further downstream applications. A key point for successful detection of specific CD4+ T cells ex vivo is the choice of a peptide/MHC II combination that results in high-affinity T Cell Receptor (TCR) binding (Benati et al., 2016). A second key point for reliable detection of MHC II tetramer-positive cells is the systematic use of a control tetramer loaded with an irrelevant peptide, with the sample and control tubes being processed in identical conditions

Comparison of the antigen sensitivity of Gag-specific CD4+ T cell responses in controlled HIV infection and HIV vaccination

Spontaneous control of HIV infection is characterized by a highly efficient cellular immune response. We showed in particular that HIV Controllers from the ANRS CO21 CODEX cohort harbor a population of specific CD4+ T cells that detect the immunodominant CD4 epitope Gag293 with high antigen sensitivity. To determine whether candidate vaccines can induce the high sensitivity responses seen in Controllers, we analyzed Gag293-specific responses in healthy volunteers who received the ADVAX DNA vaccine administered by electroporation. Comparison of Gag293-specific responses in primary CD4+ T cell lines via IFN-γ ELISpot revealed that the median antigen sensitivity in vaccinees was similar to that observed for Controllers (5x10-8 M) but higher than that in treated patients (5x10-7 M). However, antigen sensitivity remained higher in a subset of Controllers compared to vaccinees. TCR repertoire analysis of Gag293-specific CD4+ T cells from vaccinees revealed a preferential amplification of TCRβ family chain TRBV2, which also predominates in Controllers. However, TRAV family gene usage appeared more diverse in vaccinees compared to Controllers. Sequence analysis of the TCR chains amplified in 4 vaccinees revealed a biased TCR repertoire with the presence of public clonotypes (3 TRAV24 and 2 TRBV2) shared with HIV Controllers. In conclusion, DNA vaccination administered by electroporation has the potential to induce Gag-specific CD4+ T cells responses with a high antigen sensitivity and partial TCR repertoire overlap with that of Controllers. Monitoring the amplification of public TCR clonotypes could provide a novel approach to evaluate the quality of HIV vaccine responses

Specific cTfh frequency correlates with memory B cell responses in HIV controllers.

Background: Follicular helper T cells (Tfh) play an essential role in the affinity maturation of the antibody response by providing help to B cells. To determine whether this CD4+ T cell subset may contribute to the spontaneous control of HIV infection, we analyzed the phenotype and function of circulating Tfh (cTfh) in patients from the ANRS CO21 CODEX cohort who naturally controlled HIV-1 replication to undetectable levels (HIC group), and compared them to treated patients with similarly low viral loads (ART group). Methods: HIV-specific cTfh (Tet+) were detected by Gag MHC-II tetramer labeling in the CD45RA- CXCR5+ CD4+ T cell population. The function of cTfh was analyzed by the capacity to promote IgG secretion in cocultures with autologous memory B cells. Results: HIV-specific cTfh (Tet+) proved more frequent in the controller group than in the treated patient group (P=0.002). The frequency of PD-1 expression in Tet+ cTfh was increased in both groups (median >75%) compared to total cTfh (<30%), but the intensity of PD-1 expression per cell remained higher in the ART group (P=0.02), pointing to the persistence of abnormal immune activation in treated patients. The function of cTfh, analyzed in coculture with memory B cells, did not show major differences between groups in terms of total IgG production, but proved significantly more efficient in the controller group when measuring HIV-specific IgG production. The frequency of Tet+ cTfh correlated with HIV-specific IgG production (R=0.71 for Gag-specific and R=0.79 for Env-specific IgG, respectively). Conclusion: Taken together, these findings indicate that key cTfh/B cell interactions are preserved in controlled HIV infection, resulting in potent memory B cell responses that may play an underappreciated role in HIV control