CopM is a novel copper-binding protein involved in copper resistance in Synechocystis sp. PCC 6803

Copper resistance system in the cyanobacterium Synechocystis sp. PCC 6803 comprises two operons, copMRS and copBAC, which are expressed in response to copper in the media. copBAC codes for a heavy-metal efflux–resistance nodulation and division (HME-RND) system, while copMRS codes for a protein of unknown function, CopM, and a two-component system CopRS, which controls the expression of these two operons. Here, we report that CopM is a periplasmic protein able to bind Cu(I) with high affinity (KD ∼3 × 10−16). Mutants lacking copM showed a sensitive copper phenotype similar to mutants affected in copB, but lower than mutants of the two-component system CopRS, suggesting that CopBAC and CopM constitute two independent resistance mechanisms. Moreover, constitutive expression of copM is able to partially suppress the copper sensitivity of the copR mutant strain, pointing out that CopM per se is able to confer copper resistance. Furthermore, constitutive expression of copM was able to reduce total cellular copper content of the copR mutant to the levels determined in the wild-type (WT) strain. Finally, CopM was localized not only in the periplasm but also in the extracellular space, suggesting that CopM can also prevent copper accumulation probably by direct copper binding outside the cell.España, Ministerio de Economía y Competitividad BFU2010–15708España, Ministerio de Economía y Competitividad BFU2013–41712-

Redox control of copper homeostasis in cyanobacteria

Copper is essential for all living organisms but is toxic when present in excess. Therefore organisms have developed homeostatic mechanism to tightly regulate its cellular concentration. In a recent study we have shown that CopRS two-component system is essential for copper resistance in the cyanobacterium Synechocystis sp PCC 6803. This two-component regulates expression of a heavy-metal RND type copper efflux system (encoded by copBAC) as well as its own expression (in the copMRS operon) in response to an excess of copper in the media. We have also observed that both operons are induced under condition that reduces the photosynthetic electron flow and this induction depends of the presence of the copper-protein, plastocyanin. These findings, together with CopS localization to the thylakoid membrane and its periplasmic domain being able to bind copper directly, suggest that CopS could be involved in copper detection in both the periplasm and the thylakoid lume

Metals in Cyanobacteria: analysis of the copper, nickel, cobalt and arsenic homeostasis mechanisms

Traces of metal are required for fundamental biochemical processes, such as photosynthesis and respiration. Cyanobacteria metal homeostasis acquires an important role because the photosynthetic machinery imposes a high demand for metals, making them a limiting factor for cyanobacteria, especially in the open oceans. On the other hand, in the last two centuries, the metal concentrations in marine environments and lake sediments have increased as a result of several industrial activities. In all cases, cells have to tightly regulate uptake to maintain their intracellular concentrations below toxic levels. Mechanisms to obtain metal under limiting conditions and to protect cells from an excess of metals are present in cyanobacteria. Understanding metal homeostasis in cyanobacteria and the proteins involved will help to evaluate the use of these microorganisms in metal bioremediation. Furthermore, it will also help to understand how metal availability impacts primary production in the oceans. In this review, we will focus on copper, nickel, cobalt and arsenic (a toxic metalloid) metabolism, which has been mainly analyzed in model cyanobacterium Synechocystis sp. PCC 6803.info:eu-repo/semantics/publishedVersio

eggNOG 6.0: enabling comparative genomics across 12 535 organisms

The eggNOG (evolutionary gene genealogy Non-supervised Orthologous Groups) database is a bioinformatics resource providing orthology data and comprehensive functional information for organisms from all domains of life. Here, we present a major update of the database and website (version 6.0), which increases the number of covered organisms to 12 535 reference species, expands functional annotations, and implements new functionality. In total, eggNOG 6.0 provides a hierarchy of over 17M orthologous groups (OGs) computed at 1601 taxonomic levels, spanning 10 756 bacterial, 457 archaeal and 1322 eukaryotic organisms. OGs have been thoroughly annotated using recent knowledge from functional databases, including KEGG, Gene Ontology, UniProtKB, BiGG, CAZy, CARD, PFAM and SMART. eggNOG also offers phylogenetic trees for all OGs, maximising utility and versatility for end users while allowing researchers to investigate the evolutionary history of speciation and duplication events as well as the phylogenetic distribution of functional terms within each OG. Furthermore, the eggNOG 6.0 website contains new functionality to mine orthology and functional data with ease, including the possibility of generating phylogenetic profiles for multiple OGs across species or identifying single-copy OGs at custom taxonomic levels. eggNOG 6.0 is available at http://eggnog6.embl.de

eggNOG 6.0: enabling comparative genomics across 12 535 organisms

6 Pág.The eggNOG (evolutionary gene genealogy Non-supervised Orthologous Groups) database is a bioinformatics resource providing orthology data and comprehensive functional information for organisms from all domains of life. Here, we present a major update of the database and website (version 6.0), which increases the number of covered organisms to 12 535 reference species, expands functional annotations, and implements new functionality. In total, eggNOG 6.0 provides a hierarchy of over 17M orthologous groups (OGs) computed at 1601 taxonomic levels, spanning 10 756 bacterial, 457 archaeal and 1322 eukaryotic organisms. OGs have been thoroughly annotated using recent knowledge from functional databases, including KEGG, Gene Ontology, UniProtKB, BiGG, CAZy, CARD, PFAM and SMART. eggNOG also offers phylogenetic trees for all OGs, maximising utility and versatility for end users while allowing researchers to investigate the evolutionary history of speciation and duplication events as well as the phylogenetic distribution of functional terms within each OG. Furthermore, the eggNOG 6.0 website contains new functionality to mine orthology and functional data with ease, including the possibility of generating phylogenetic profiles for multiple OGs across species or identifying single-copy OGs at custom taxonomic levels. eggNOG 6.0 is available at http://eggnog6.embl.de.National Programme for Fostering Excellence in Scientific and Technical Research [PGC2018-098073-A-I00 MCIU/AEI/FEDER, UE to J.H.-C., J.G.-L.]; Chan Zuckerberg Initiative DAF [2020-218584]; Silicon Valley Community Foundation (to J.B. and J.H.C.); Severo Ochoa Centres of Excellence Programme from the State Research Agency (AEI) of Spain [SEV-2016–0672 (2017–2021) to C.P.C.]; Research Technical Support Staff Aid [PTA2019-017593-I/AEI/10.13039/501100011033 to A.H.P.]; Novo Nordisk Foundation [NNF14CC0001 to R.K., L.J.J.]; SIB Swiss Institute of Bioinformatics (to D.S. and C.vM.). Funding for open access charge: Institutional CSIC and EMBL agreements.Peer reviewe

Functional and evolutionary significance of unknown genes from uncultivated taxa

25 Pág.Many of the Earth's microbes remain uncultured and understudied, limiting our understanding of the functional and evolutionary aspects of their genetic material, which remain largely overlooked in most metagenomic studies1. Here we analysed 149,842 environmental genomes from multiple habitats2-6 and compiled a curated catalogue of 404,085 functionally and evolutionarily significant novel (FESNov) gene families exclusive to uncultivated prokaryotic taxa. All FESNov families span multiple species, exhibit strong signals of purifying selection and qualify as new orthologous groups, thus nearly tripling the number of bacterial and archaeal gene families described to date. The FESNov catalogue is enriched in clade-specific traits, including 1,034 novel families that can distinguish entire uncultivated phyla, classes and orders, probably representing synapomorphies that facilitated their evolutionary divergence. Using genomic context analysis and structural alignments we predicted functional associations for 32.4% of FESNov families, including 4,349 high-confidence associations with important biological processes. These predictions provide a valuable hypothesis-driven framework that we used for experimental validatation of a new gene family involved in cell motility and a novel set of antimicrobial peptides. We also demonstrate that the relative abundance profiles of novel families can discriminate between environments and clinical conditions, leading to the discovery of potentially new biomarkers associated with colorectal cancer. We expect this work to enhance future metagenomics studies and expand our knowledge of the genetic repertory of uncultivated organisms.This project has received funding from the National Programme for Fostering Excellence in Scientific and Technical Research (grant no. PGC2018-098073-A-I00 MCIU/AEI/FEDER, UE) and, partially, by MCIN/AEI/10.13039/501100011033/ and FEDER Una manera de hacer Europa (grant no. PID2021-127210NB-I00). A.R.d.R. was supported by a fellowship from la Caixa Foundation (ID 100010434, fellowship code no. LCF/BQ/DI18/11660009), cofunded by the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 713673. C.P.C., S.S.-H. and Z.D. acknowledge support by Severo Ochoa Centres of Excellence Programme from the State Research Agency of Spain (grant nos. SEV-2016-0672 (2017–2021) and CEX2020-000999-S). J.B. acknowledges support by a grant from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (no. 2020-218584). A.H.-P. was supported by Research Technical Support Staff Aid (no. PTA2019-017593-I/AEI/10.13039/501100011033). M.M.-P., J.J.R.-H. and E.L.-S. acknowledge support from Ministerio de Ciencia e Innovación, MCIN/AEI/10.13039/501100011033 (grant no. PID2021-125673OB-I00). S.S. acknowledges support from the Swiss National Science Foundation project (grant no. 205321_184955) and NCCR Microbiomes (no. 51NF40_180575), and thanks the staff at ETH Zurich IT Services and HPC facilities.Peer reviewe

Towards the biogeography of prokaryotic genes

Funding was provided by the European Union’s Horizon 2020 Research and Innovation Programme (grant 686070: DD-DeCaF to P.B.) and Marie Skłodowska-Curie Actions (grant 713673 to A.R.d.R.), the European Research Council (ERC) MicrobioS (ERC-AdG-669830 to P.B.), JTC project jumpAR (01KI1706 to P.B.), a BMBF Grant (grant 031L0181A: LAMarCK to P.B.), the European Molecular Biology Laboratory (P.B.), the ETH and Helmut Horten Foundation (S.S.), the National Key R&D Program of China (grant 2020YFA0712403 to X.-M.Z.), (grant 61932008 to X.-M.Z.; grant 61772368 to X.-M.Z.; grant 31950410544 to L.P.C.), the Shanghai Municipal Science and Technology Major Project (grant 2018SHZDZX01 to X.-M.Z. and L.P.C.) and Zhangjiang Lab (X.-M.Z. and L.P.C.), the International Development Research Centre (grant 109304, EMBARK under the JPI AMR framework; to L.P.C.), la Caixa Foundation (grant 100010434, fellowship code LCF/BQ/DI18/11660009 to A.R.d.R.), the Severo Ochoa Program for Centres of Excellence in R&D from the Agencia Estatal de Investigación of Spain (grant SEV-2016-0672 (2017–2021) to C.P.C.), the Ministerio de Ciencia, Innovación y Universidades (grant PGC2018-098073-A-I00 MCIU/AEI/FEDER to J.H.-C. and J.G.-L.), the Innovation Fund Denmark (grant 4203-00005B, PNM), the Biotechnology and Biological Sciences research Council (BBSrC) Gut MicroInstitute Strategic Programmebes and Health BB/r012490/1 and its constituent project BBS/e/F/000Pr10355 (F.H.). R.A. is a member of the Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences.Peer reviewe

CopM is a novel copper-binding protein involved in copper resistance in Synechocystis sp. PCC 6803.

Copper resistance system in the cyanobacterium Synechocystis sp. PCC 6803 comprises two operons, copMRS and copBAC, which are expressed in response to copper in the media. copBAC codes for a heavy-metal efflux-resistance nodulation and division (HME-RND) system, while copMRS codes for a protein of unknown function, CopM, and a two-component system CopRS, which controls the expression of these two operons. Here, we report that CopM is a periplasmic protein able to bind Cu(I) with high affinity (KD ~3 × 10(-16) ). Mutants lacking copM showed a sensitive copper phenotype similar to mutants affected in copB, but lower than mutants of the two-component system CopRS, suggesting that CopBAC and CopM constitute two independent resistance mechanisms. Moreover, constitutive expression of copM is able to partially suppress the copper sensitivity of the copR mutant strain, pointing out that CopM per se is able to confer copper resistance. Furthermore, constitutive expression of copM was able to reduce total cellular copper content of the copR mutant to the levels determined in the wild-type (WT) strain. Finally, CopM was localized not only in the periplasm but also in the extracellular space, suggesting that CopM can also prevent copper accumulation probably by direct copper binding outside the cell.Peer reviewe

Exploring the sediment-associated microbiota of the Mar Menor coastal lagoon

7 Pág.Coastal lagoons represent transitional ecosystems between terrestrial and marine environments and play a central role in nutrient cycling, carbon flux, and biodiversity conservation (Kjerfve, 1994; Schubert and Telesh, 2017). These characteristics and their location on low-lying coasts are responsible for coastal lagoons being among the most productive and valuable ecosystems in the world, providing and supporting a wide range of ecological services and social benefits (Pérez-Ruzafa et al., 2020). Coastal lagoons are classified as one of the most sensitive ecosystems to changes in their environment (Velasco et al., 2018) especially to anthropogenic eutrophication and pollutant accumulation (Barbier et al., 2011), which explains why most coastal lagoons around the world show signs of ecological imbalance and degradation. Marine coastal sediments are complex ecosystems that are influenced by the interaction of various geological, hydrological, physical, chemical and biological factors (Zhang et al., 1999). Coastal sediments formed by continental transport and sedimentation of biological products provide abundant nutrients for microorganisms (Parkes et al., 2014). In coastal marine ecosystems, microorganisms play a central role in shaping nutrient dynamics and biogeochemical cycles by transforming and metabolizing nutrients and pollutants (Nogales et al., 2011). Microorganisms can degrade sediment organic matter, promote sulfate reduction, sulfide/sulfur oxidation, iron reduction, nitrification and pollutant degradation, improve sediment structure and increase the stability of ecosystems (Behera et al., 2017). However, microorganisms in coastal sediments are influenced by the physico-chemical properties of the sediment, including salinity, pH, nutrients and are especially vulnerable to pollutants (Rodríguez et al., 2018; Liang et al., 2023). Changes in these properties can have a cascading effect on the microbial growth, metabolism, and activity, thereby affecting the structure of the sediment-associated microbial communities (Jackson and Vallaire, 2009; Liang et al., 2023). The Mar Menor, located in the southeast of Spain, is the largest hypersaline coastal lagoon in Europe, with a surface area of 135 km2 (Conesa and Jiménez-Cárceles, 2007). The lagoon and its adjacent areas are protected at the national and international levels. Mar Menor is included in the Ramsar wetland sites of international importance and the Specially Protected Areas of Mediterranean Importance [SPAMI; (Álvarez-Rogel et al., 2020)]. In recent years, increasing human activities, especially mining, agriculture and tourism, have caused significant negative changes in the Mar Menor, leading to a considerable input of sediments, nutrients (nitrates and phosphates) and pollutants (pesticides and metals) into the lagoon (Velasco et al., 2006; Pérez-Ruzafa et al., 2019). These activities have caused a decline in water quality, leading to the proliferation of harmful algal blooms, fish mortality events, and degradation of seagrass beds (Pérez Ruzafa et al., 2004; Pérez-Ruzafa et al., 2006; Zamora-López et al., 2022). In 2015, the ecological condition of the lagoon deteriorated significantly due to a massive phytoplankton bloom, resulting in the loss of macrophytes and benthic fauna (Ruiz-Fernández et al., 2019). This disturbance destabilized the natural ecological balance of the lagoon leading to several hypoxic episodes in recent years (Álvarez-Rogel et al., 2020). Many of these negative impacts could also affect the sediment-associated microbiota, which is not only an important contributor to biogeochemical cycles but could also help to counteract these impacts by accumulating and managing nutrients and contaminants (Dash et al., 2013; Nzila, 2013; Rodríguez et al., 2018). However, our knowledge of the microbial communities in the Mar Menor remains quite limited (Aldeguer-Riquelme et al., 2022). This study aims to preliminarily characterize the microbial communities in different zones of the Mar Menor impacted by tourism, mining, or agricultural activities. Its objective is to identify microbial biomarkers that serve as indicators of the lagoon’s environmental conditions. We anticipate that these findings will provide valuable insight into the microbial biosphere of the region and make a significant contribution to the establishment of effective conservation and management practices for the sustainability of this important ecosystem.The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by the PADI Foundation [project 75263 to JG-L] and the National Programme for Fostering Excellence in Scientific and Technical Research [PID2021-127210NB-I00 MCIU/AEI/FEDER, UE to JH-C and JG-L].Peer reviewe

Table_2_Exploring the sediment-associated microbiota of the Mar Menor coastal lagoon.xlsx

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