Functional metagenomics reveals differential chitin degradation and utilization features across free-living and host-associated marine microbiomes

BACKGROUND

Chitin ranks as the most abundant polysaccharide in the oceans yet knowledge of shifts in structure and diversity of chitin-degrading communities across marine niches is scarce. Here, we integrate cultivation-dependent and -independent approaches to shed light on the chitin processing potential within the microbiomes of marine sponges, octocorals, sediments, and seawater.

RESULTS

We found that cultivatable host-associated bacteria in the genera Aquimarina, Enterovibrio, Microbulbifer, Pseudoalteromonas, Shewanella, and Vibrio were able to degrade colloidal chitin in vitro. Congruent with enzymatic activity bioassays, genome-wide inspection of cultivated symbionts revealed that Vibrio and Aquimarina species, particularly, possess several endo- and exo-chitinase-encoding genes underlying their ability to cleave the large chitin polymer into oligomers and dimers. Conversely, Alphaproteobacteria species were found to specialize in the utilization of the chitin monomer N-acetylglucosamine more often. Phylogenetic assessments uncovered a high degree of within-genome diversification of multiple, full-length endo-chitinase genes for Aquimarina and Vibrio strains, suggestive of a versatile chitin catabolism aptitude. We then analyzed the abundance distributions of chitin metabolism-related genes across 30 Illumina-sequenced microbial metagenomes and found that the endosymbiotic consortium of Spongia officinalis is enriched in polysaccharide deacetylases, suggesting the ability of the marine sponge microbiome to convert chitin into its deacetylated-and biotechnologically versatile-form chitosan. Instead, the abundance of endo-chitinase and chitin-binding protein-encoding genes in healthy octocorals leveled up with those from the surrounding environment but was found to be depleted in necrotic octocoral tissue. Using cultivation-independent, taxonomic assignments of endo-chitinase encoding genes, we unveiled previously unsuspected richness and divergent structures of chitinolytic communities across host-associated and free-living biotopes, revealing putative roles for uncultivated Gammaproteobacteria and Chloroflexi symbionts in chitin processing within sessile marine invertebrates.

CONCLUSIONS

Our findings suggest that differential chitin degradation pathways, utilization, and turnover dictate the processing of chitin across marine micro-niches and support the hypothesis that inter-species cross-feeding could facilitate the co-existence of chitin utilizers within marine invertebrate microbiomes. We further identified chitin metabolism functions which may serve as indicators of microbiome integrity/dysbiosis in corals and reveal putative novel chitinolytic enzymes in the genus Aquimarina that may find applications in the blue biotechnology sector. Video abstract.

Palantir: a springboard for the analysis of secondary metabolite gene clusters in large-scale genome mining projects

SUMMARY

To support small and large-scale genome mining projects, we present Post-processing Analysis tooLbox for ANTIsmash Reports (Palantir), a dedicated software suite for handling and refining secondary metabolite biosynthetic gene cluster (BGC) data annotated with the popular antiSMASH pipeline. Palantir provides new functionalities building on NRPS/PKS predictions from antiSMASH, such as improved BGC annotation, module delineation and easy access to sub-sequences at different levels (cluster, gene, module and domain). Moreover, it can parse user-provided antiSMASH reports and reformat them for direct use or storage in a relational database.

AVAILABILITY AND IMPLEMENTATION

Palantir is released both as a Perl API available on CPAN (https://metacpan.org/release/Bio-Palantir) and as a web application (http://palantir.uliege.be). As a practical use case, the web interface also features a database built from the mining of 1616 cyanobacterial genomes, of which 1488 were predicted to encode at least one BGC.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

[Management of immune-related toxicities associated with immune checkpoints inhibitors: Data from the multidisciplinary meeting « ToxImmun » in Eastern Occitania]

Immune checkpoint inhibitors (ICIs) can cause numerous and complex immune-related adverse events whose management need a multidisciplinary approach. Herein, we investigated 114 requests, mostly concerning patients suffering from lung cancer, that were submitted to the « ToxImmun » multidisciplinary meeting in Eastern Occitania between December the 17th 2018 and January the 20th 2020. The leading reasons for the request concerned the putative causal link between immunotherapy and immune-toxicity and its management, followed by possible retreatment after temporary withdrawn because of adverse event, and finally the possibility to initiate ICIs in patients with pre-existing autoimmunity. Colitis, hepatitis and myocarditis were the most frequent immune-related adverse events (IRAEs), both all grade and grade 3-4. Sicca syndrome (with or without Sjogren criteria) was also frequent (26% of cases) and seems to be associated with severe toxicity and multi-toxicity. The mean time to first IRAE was 3.8 months, a time shortened with the use of anti-PD-L1 agents or ICI combination. A majority of requests came from initial evaluation by the internist confirming the early and main role of this specialty in the management of immunotoxicity. Expansion of this regional multidisciplinary meeting, coordinated by internists and medical oncologists, could improve management of immune-related adverse events for the patients' benefits.

Nonribosomal peptides in fungal cell factories: from genome mining to optimized heterologous production

Fungi are notoriously prolific producers of secondary metabolites including nonribosomal peptides (NRPs). The structural complexity of NRPs grants them interesting activities such as antibiotic, anti-cancer, and anti-inflammatory properties. The discovery of these compounds with attractive activities can be achieved by using two approaches: either by screening samples originating from various environments for their biological activities, or by identifying the related clusters in genomic sequences thanks to bioinformatics tools. This genome mining approach has grown tremendously due to recent advances in genome sequencing, which have provided an incredible amount of genomic data from hundreds of microbial species. Regarding fungal organisms, the genomic data have revealed the presence of an unexpected number of putative NRP-related gene clusters. This highlights fungi as a goldmine for the discovery of putative novel bioactive compounds. Recent development of NRP dedicated bioinformatics tools have increased the capacity to identify these gene clusters and to deduce NRPs structures, speeding-up the screening process for novel metabolites discovery. Unfortunately, the newly identified compound is frequently not or poorly produced by native producers due to a lack of expression of the related genes cluster. A frequently employed strategy to increase production rates consists in transferring the related biosynthetic pathway in heterologous hosts. This review aims to provide a comprehensive overview about the topic of NRPs discovery, from gene cluster identification by genome mining to the heterologous production in fungal hosts. The main computational tools and methods for genome mining are herein presented with an emphasis on the particularities of the fungal systems. The different steps of the reconstitution of NRP biosynthetic pathway in heterologous fungal cell factories will be discussed, as well as the key factors to consider for maximizing productivity. Several examples will be developed to illustrate the potential of heterologous production to both discover uncharacterized novel compounds predicted in silico by genome mining, and to enhance the productivity of interesting bio-active natural products.

Psoriatic epidermis is associated with upregulation of CDK2 and inhibition of CDK4 activity

BACKGROUND

The cyclin-dependent kinases (CDKs) CDK2 and CDK4 are involved in regulation of cell-cycle progression, and psoriasis is characterized by hyperproliferation of basal epidermal cells. CDK inhibitory proteins (CKIs) such as p16^{INK 4A} (p16) bind CDK4/6 kinases and prevent their interaction with D-type cyclins. CKIs such as p21^Cip1 (p21) and p27^Kip1 (p27) associate with CDK-cyclin complexes and prevent their activation.

OBJECTIVES

To gain insight into the molecular implication of CDK2 and CDK4 kinases in psoriasis, we sought to characterize expression of these kinases and associated cyclins, as well as of CKIs, and addressed the status of CDK2 and CDK4 activity in human psoriatic epidermis.

METHODS

A cohort of 24 patients with psoriasis participated in the study. Biopsies were removed from a chronic plaque and from nonlesional skin. CDK2, CDK4, cyclin D1, cyclin E and CKI protein expression was assessed by immunoblotting, immunohistochemistry and immunofluorescence. CDK4 and CDK2 mRNA expression was determined by real-time polymerase chain reaction. Specific kinase activities of CDK2 and CDK4 were evaluated using fluorescent peptide biosensors.

RESULTS

CDK2-cyclin E expression and activity were significantly increased in psoriatic epidermis compared with uninvolved adjacent skin. In contrast, CDK4-cyclin D1 activity was inhibited, although its expression was increased in psoriatic epidermis and its transcription slightly inhibited. p27 expression was reduced, while p16 and p21 expression was induced in psoriatic epidermis.

CONCLUSIONS

Epidermal CDK2 activity is increased in psoriatic epidermis while CDK4 activity is completely inhibited. These alterations are not associated with changes in CDK transcription and instead involve post-translational control mediated by decreased expression of p27 and p16 overexpression, respectively. What's already known about this topic? Cyclin-dependent kinases (CDKs) are involved in cell-cycle progression. The levels of cyclin partners and CDK inhibitors regulate their activity. Psoriasis is a chronic T-cell-driven inflammatory skin disease characterized by hyperproliferation of basal epidermal cells. What does this study add? Thanks to fluorescent peptide biosensors, this study demonstrates that epidermal CDK2 activity is increased in psoriatic epidermis while CDK4 activity is completely inhibited. These alterations involve post-translational control mediated by decreased expression of p27, and p16 overexpression, respectively. What is the translational message? CDK2 and CDK4 are involved in regulation of cell-cycle progression, and psoriasis is characterized by hyperproliferation of basal epidermal cells. Epidermal CDK2 activity is increased in psoriatic epidermis while CDK4 activity is completely inhibited. These alterations are not associated with changes in CDK transcription and instead involve post-translational control mediated by decreased expression of p27 and p16 overexpression, respectively. Pharmacological modulation of CDK2 and CDK4 may constitute a promising therapeutic strategy.

Consensus assessment of the contamination level of publicly available cyanobacterial genomes

Publicly available genomes are crucial for phylogenetic and metagenomic studies, in which contaminating sequences can be the cause of major problems. This issue is expected to be especially important for Cyanobacteria because axenic strains are notoriously difficult to obtain and keep in culture. Yet, despite their great scientific interest, no data are currently available concerning the quality of publicly available cyanobacterial genomes. As reliably detecting contaminants is a complex task, we designed a pipeline combining six methods in a consensus strategy to assess the contamination level of 440 genome assemblies of Cyanobacteria. Two methods are based on published reference databases of ribosomal genes (SSU rRNA 16S and ribosomal proteins), one is indirectly based on a reference database of marker genes (CheckM), and three are based on complete genome analysis. Among those genome-wide methods, Kraken and DIAMOND blastx share the same reference database that we derived from Ensembl Bacteria, whereas CONCOCT does not require any reference database, instead relying on differences in DNA tetramer frequencies. Given that all the six methods appear to have their own strengths and limitations, we used the consensus of their rankings to infer that >5% of cyanobacterial genome assemblies are highly contaminated by foreign DNA (i.e., contaminants were detected by 5 or 6 methods). Our results will help researchers to check the quality of publicly available genomic data before use in their own analyses. Moreover, we argue that journals should make mandatory the submission of raw read data along with genome assemblies in order to facilitate the detection of contaminants in sequence databases.

Performances of an Artificial Reagent for the One-stage Factor IX Assay

A mixture of adsorbed normal human plasma and chicken plasma was prepared as reagent for factor IX measurement using a one-stage method. The substrate was found to be specific for factor IX. Its performances tested on samples displaying factor IX activity ranging from <l%–2,500% compared favorably with those obtained when using the plasma of severe haemophilia B patients as substrate.

The Cdc42/Rac1 regulator CdGAP is a novel E-cadherin transcriptional co-repressor with Zeb2 in breast cancer

The loss of E-cadherin causes dysfunction of the cell-cell junction machinery, which is an initial step in epithelial-to-mesenchymal transition (EMT), facilitating cancer cell invasion and the formation of metastases. A set of transcriptional repressors of E-cadherin (CDH1) gene expression, including Snail1, Snail2 and Zeb2 mediate E-cadherin downregulation in breast cancer. However, the molecular mechanisms underlying the control of E-cadherin expression in breast cancer progression remain largely unknown. Here, by using global gene expression approaches, we uncover a novel function for Cdc42 GTPase-activating protein (CdGAP) in the regulation of expression of genes involved in EMT. We found that CdGAP used its proline-rich domain to form a functional complex with Zeb2 to mediate the repression of E-cadherin expression in ErbB2-transformed breast cancer cells. Conversely, knockdown of CdGAP expression led to a decrease of the transcriptional repressors Snail1 and Zeb2, and this correlated with an increase in E-cadherin levels, restoration of cell-cell junctions, and epithelial-like morphological changes. In vivo, loss of CdGAP in ErbB2-transformed breast cancer cells impaired tumor growth and suppressed metastasis to lungs. Finally, CdGAP was highly expressed in basal-type breast cancer cells, and its strong expression correlated with poor prognosis in breast cancer patients. Together, these data support a previously unknown nuclear function for CdGAP where it cooperates in a GAP-independent manner with transcriptional repressors to function as a critical modulator of breast cancer through repression of E-cadherin transcription. Targeting Zeb2-CdGAP interactions may represent novel therapeutic opportunities for breast cancer treatment.

[Type I interferonopathies]

Type I interferonopathies are a group of Mendelian disorders characterized by a common physiopathology: the up-regulation of type I interferons. To date, interferonopathies include Aicardi-Goutières syndrome, familial chilblain lupus, spondyenchondromatosis, PRoteasome-associated auto-inflammatory syndrome (PRAAS) and Singleton-Merten syndrome. These diseases present phenotypic overlap including cutaneous features like chilblain lupus, that can be inaugural or present within the first months of life. This novel set of inborn errors of immunity is evolving rapidly, with recognition of new diseases and genes. Recent and improved understanding of the physiopathology of overexpression of type I interferons has allowed the development of targeted therapies, currently being evaluated, like Janus-kinases or reverse transcriptase inhibitors.

Gekoppelte periodische Elektrodenvorgänge

Es wird gezeigt, wie periodisch reagierende Elektroden in analoger Weise wie elektrische Schwingungskreise miteinander gekoppelt werden können. Die dabei auftretenden Kopplungsschwingungen zeichnen sich durch eine ausgeprägte Tendenz zur Synchronisierung aus, die auch dann noch angestrebt wird, wenn diese im Falle zu geringer Kopplungsfestigkeit aus energetischen Gründen nicht mehr vollständig möglich ist. Es entstehen auf diese Weise mannigfaltige Synchronisierungsformen, die eine auffallende Übereinstimmung mit biologischen rhythmischen Erscheinungen zeigen. Diese Analogie beruht auf der Kippschwingungsnatur beider Schwingungsphänomene. So stimmen die hier an elektrochemischen Systemen erhaltenen Oszillogramme auch weitgehend mit denen überein, die B. van der Pol und U. van der Mark sowie A. Bethe bei Modellversuchen zur biologischen Rhythmizität mit gekoppelten elektrischen Kippschwingungskreisen gefunden haben.

[Multiple primary cutaneous plasmacytoma]

BACKGROUND

Primary cutaneous plasmacytoma is a rare form of cutaneous B-cell lymphoma.

PATIENTS AND METHODS

A 51 year-old male with an unremarkable history gradually presented erythematous papulonodular lesions that had appeared gradually over the whole body throughout a two-year period and showing histologic and immunohistochemical features of cutaneous plasmacytoma. Staging investigations confirmed the primary character of the disease, and because of this and the absence of functional impairment, we opted for therapeutic abstention. No progression was noted after 4 years of regular monitoring.

DISCUSSION

Primary cutaneous plasmacytoma (PCP) is characterized by clonal proliferation of plasma cells in skin. Multiple PCPs are extremely rare and to date have been treated in most cases by chemotherapy, either with or without radiotherapy. The prognosis is poor, with 2-year survival of only 25%. The present case is original, being the only one to our knowledge in which therapeutic abstention was followed by a lack of progression after 4 years of regular follow-up. Consequently, certain indolent forms of PCP do not warrant automatic institution of chemotherapy.

[Necrotic arachnidism in the south of France: two clinical cases of loxoscelism]

BACKGROUND

loxosceles spiders are found throughout the world and are responsible for numerous cases of envenomation in America and Southern Europe. We describe, to our knowledge for the first time in France, two clinical cases of cutaneous loxoscelism.

CASE REPORT

two cases of skin necrosis arising after supposed spider bites were grouped together because of their similar clinical presentation: an initial painless bite and rapid development of an inflammatory and painful cutaneous lesion with a central hemorrhagic bulla surrounded by a perimeter of blanched skin (the "red, white, and blue" sign). The outcome in both cases was deep skin necrosis and chronic ulceration requiring surgical treatment.

DISCUSSION

loxoscelism can result in dermonecrosis. Although our cases were not documented by capture of the spider, the diagnosis of cutaneous loxoscelism was supported by the characteristic appearance of the lesion, a typical clinical course, elimination of differential diagnoses, and the confirmed presence of Loxosceles rufescens in the region.

CONCLUSION

loxoscelism can occur in the south of France and although rare, must be considered in this region as a possible cause of skin necrosis.

[Neonatal Volkmann's syndrome]

BACKGROUND

Acute limb compartment syndrome or Volkmann's ischaemic contracture is an acquired ischaemia of nerve and muscle causes by raised pressure within a closed fascial space. Congenital Volkmann's ischaemic contracture (CVIC) is a rare entity.

PATIENTS AND METHODS

A 2-day-old girl was referred with a problem of the left forearm and arm, which exhibited cold oedema with decreased mobility. Lesions were present at birth and were rapidly complicated by skin necrosis. The mother was taking olazanpine, prazepam and valpromide throughout the entire pregnancy. Delivery was complicated by shoulder dystocia requiring obstetric procedures such as suprapubic pressure, Couder's maneuver and episiotomy. On physical examination her left hemi-thorax, left arm, forearm and hand exhibited marked oedema. A large and well-demarcated bullous, fibrous and ulcerated area of skin necrosis was observed on the elbow fold and on the inner anterior part of the arm. Digital flexion with cyanosis was present. MR angiography revealed extensive oedema of the soft tissue and muscle with fascial effusion, associated with compression of the arm arteries and reduced blood flow in the forearm. A fasciotomy was performed at Day 3 of life. The postsurgical arterial MRI was normal. At Day 10 of life, the patient developed opisthotonos involving spasms and tremors associated with numerous intercritical abnormalities evoking benzodiazepine weaning syndrome. The child's neurological status was stabilized by treatment with phenobarbital and clonazepam. She was subsequently lost to follow-up.

DISCUSSION

CVIC has been ascribed to multiples causes. Mechanical compression is the main recognized factor: amniotic band constriction, umbilical cord loops, compression in utero by a deceased co-twin, malposition of the hand, arm or forearm, local or general factors that can add to extraction problems: brachypelvic disproportion, extraction with forceps, oligo/polyhydramnios, pre-term delivery, pre-eclampsia, caesarean section, premature labour, excessive maternal weight gain or diabetes. Our case emphasized three main points. First, the diagnostic value of early MR angiography in the event of associated extensive tissue oedema, multiple arterial compression and decreased vascular perfusion. Second, the role of shoulder dystocia in triggering the traumatic factor reported for the first time. Third, the role of neuroleptic and anxiolytic treatments taken by the mother during pregnancy. Prazepam is a long-acting benzodiazepine that can cause impregnation and withdraw syndromes in neonates. Impregnation "floppy infant syndrome" is an early event characterized by hypotonia, hypoventilation and lethargy. Hypotonia and decreased foetal movements may favour prolonged pressures and malposition with secondary crush injury during delivery. Maternal medication has not been cited hitherto as an aetiological factor in neonatal compartment syndrome.