Expression of multiplecbb3cytochromecoxidase isoforms by combinations of multiple isosubunits inPseudomonas aeruginosa

The ubiquitous opportunistic human pathogenPseudomonas aeruginosahas five terminal oxidases for aerobic respiration and uses them under different growth conditions. Two of them arecbb3-type cytochromecoxidases encoded by the gene clustersccoN1O1Q1P1andccoN2O2Q2P2, which are the main terminal oxidases under high- and low-oxygen conditions, respectively.P. aeruginosaalso has two orphan gene clusters,ccoN3Q3andccoN4Q4, encoding the core catalytic CcoN isosubunits, but the roles of these genes have not been clarified. We found that 16 activecbb3isoforms could be produced by combinations of four CcoN, two CcoO, and two CcoP isosubunits. The CcoN3- or CcoN4-containing isoforms were produced in the WT cell membrane in response to nitrite and cyanide, respectively. The strains carrying these isoforms were more resistant to nitrite or cyanide under low-oxygen conditions. These results indicate thatP. aeruginosagains resistance to respiratory inhibitors using multiplecbb3isoforms with different features, which are produced through exchanges of multiple core catalytic isosubunits.

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Crystal structure of NirF: Insights into its role in heme d1 biosynthesis

10.1101/2020.01.13.904656 ◽

2020 ◽

Author(s):

Thomas Klünemann ◽

Manfred Nimtz ◽

Lothar Jänsch ◽

Gunhild Layer ◽

Wulf Blankenfeldt

Keyword(s):

Ligand Binding Site ◽

Human Pathogen ◽

X Ray ◽

The Core ◽

X Ray Scattering ◽

Anoxic Environments ◽

Opportunistic Human Pathogen ◽

Heme D1 ◽

Membrane Anchoring

AbstractCertain facultative anaerobes such as the opportunistic human pathogen Pseudomonas aeruginosa can respire on nitrate, a process generally known as denitrification. This enables denitrifying bacteria to survive in anoxic environments and contributes e.g. to the formation of biofilm, hence increasing difficulties in eradicating P. aeruginosa infections. A central step in denitrification is the reduction of nitrite to nitrous oxide by nitrite reductase NirS, an enzyme that requires the unique cofactor heme d1. While heme d1 biosynthesis is mostly understood, the role of the essential periplasmatic protein NirF in this pathway remains unclear. Here, we have determined crystal structures of NirF and its complex with dihydroheme d1, the last intermediate of heme d1 biosynthesis. We found that NirF forms a bottom-to-bottom β-propeller homodimer and confirmed this by multi-angle light and small-angle X-ray scattering. The N-termini are immediately neighbored and project away from the core structure, which hints at simultaneous membrane anchoring via both N-termini. Further, the complex with dihydroheme d1 allowed us to probe the importance of specific residues in the vicinity of the ligand binding site, revealing residues not required for binding or stability of NirF but essential for denitrification in experiments with complemented mutants of a ΔnirF strain of P. aeruginosa. Together, these data implicate that NirF possesses a yet unknown enzymatic activity and is not simply a binding protein of heme d1 derivatives.

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The Production of hydrogen Sulphide and the Effects of Nitric Oxide (NO) and Low Oxygen Conditions in Intrauterine Tissues in Rats

Bulletin of Egyptian Society for Physiological Sciences ◽

10.21608/besps.2009.36719 ◽

2009 ◽

Vol 29 (2) ◽

pp. 195-206

Author(s):

Saad El-Sekelly ◽

Mohamed Mahmoud ◽

Morsy Matar

Keyword(s):

Nitric Oxide ◽

Hydrogen Sulphide ◽

Low Oxygen ◽

Production Of Hydrogen ◽

Oxygen Conditions

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Analysis of the chromosomal clustering of Fusarium-responsive wheat genes uncovers new players in the defence against head blight disease

Scientific Reports ◽

10.1038/s41598-021-86362-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Alexandre Perochon ◽

Harriet R. Benbow ◽

Katarzyna Ślęczka-Brady ◽

Keshav B. Malla ◽

Fiona M. Doohan

Keyword(s):

Map Kinases ◽

Gene Families ◽

Gene Clusters ◽

Head Blight ◽

Orphan Gene ◽

Metabolic Genes ◽

Eukaryotic Gene ◽

Blight Disease ◽

Genomic Regions ◽

Eukaryotic Genomes

AbstractThere is increasing evidence that some functionally related, co-expressed genes cluster within eukaryotic genomes. We present a novel pipeline that delineates such eukaryotic gene clusters. Using this tool for bread wheat, we uncovered 44 clusters of genes that are responsive to the fungal pathogen Fusarium graminearum. As expected, these Fusarium-responsive gene clusters (FRGCs) included metabolic gene clusters, many of which are associated with disease resistance, but hitherto not described for wheat. However, the majority of the FRGCs are non-metabolic, many of which contain clusters of paralogues, including those implicated in plant disease responses, such as glutathione transferases, MAP kinases, and germin-like proteins. 20 of the FRGCs encode nonhomologous, non-metabolic genes (including defence-related genes). One of these clusters includes the characterised Fusarium resistance orphan gene, TaFROG. Eight of the FRGCs map within 6 FHB resistance loci. One small QTL on chromosome 7D (4.7 Mb) encodes eight Fusarium-responsive genes, five of which are within a FRGC. This study provides a new tool to identify genomic regions enriched in genes responsive to specific traits of interest and applied herein it highlighted gene families, genetic loci and biological pathways of importance in the response of wheat to disease.

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CRISPR-based transcriptional activation tool for silent genes in filamentous fungi

Scientific Reports ◽

10.1038/s41598-020-80864-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

László Mózsik ◽

Mirthe Hoekzema ◽

Niels A. W. de Kok ◽

Roel A. L. Bovenberg ◽

Yvonne Nygård ◽

...

Keyword(s):

Filamentous Fungi ◽

Transcriptional Activation ◽

Core Promoter ◽

Crop Protection ◽

Gene Clusters ◽

Growth Conditions ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

Fluorescent Reporter ◽

A Genome

AbstractFilamentous fungi are historically known to be a rich reservoir of bioactive compounds that are applied in a myriad of fields ranging from crop protection to medicine. The surge of genomic data available shows that fungi remain an excellent source for new pharmaceuticals. However, most of the responsible biosynthetic gene clusters are transcriptionally silent under laboratory growth conditions. Therefore, generic strategies for activation of these clusters are required. Here, we present a genome-editing-free, transcriptional regulation tool for filamentous fungi, based on the CRISPR activation (CRISPRa) methodology. Herein, a nuclease-defective mutant of Cas9 (dCas9) was fused to a highly active tripartite activator VP64-p65-Rta (VPR) to allow for sgRNA directed targeted gene regulation. dCas9-VPR was introduced, together with an easy to use sgRNA “plug-and-play” module, into a non-integrative AMA1-vector, which is compatible with several filamentous fungal species. To demonstrate its potential, this vector was used to transcriptionally activate a fluorescent reporter gene under the control of the penDE core promoter in Penicillium rubens. Subsequently, we activated the transcriptionally silent, native P. rubens macrophorin biosynthetic gene cluster by targeting dCas9-VPR to the promoter region of the transcription factor macR. This resulted in the production of antimicrobial macrophorins. This CRISPRa technology can be used for the rapid and convenient activation of silent fungal biosynthetic gene clusters, and thereby aid in the identification of novel compounds such as antimicrobials.

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A plant endophyte Staphylococcus hominis strain MBL_AB63 produces a novel lantibiotic, homicorcin and a position one variant

Scientific Reports ◽

10.1038/s41598-021-90613-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

M. Aftab Uddin ◽

Shammi Akter ◽

Mahbuba Ferdous ◽

Badrul Haidar ◽

Al Amin ◽

...

Keyword(s):

Gene Clusters ◽

Antimicrobial Activities ◽

Whole Genome Sequence ◽

Antimicrobial Substances ◽

The Core ◽

Rp Hplc ◽

Ring Structures ◽

Core Peptide ◽

Staphylococcus Hominis ◽

Epilancin 15X

AbstractHere we report a jute endophyte Staphylococcus hominis strain MBL_AB63 isolated from jute seeds which showed promising antimicrobial activity against Staphylococcus aureus SG511 when screening for antimicrobial substances. The whole genome sequence of this strain, annotated using BAGEL4 and antiSMASH 5.0 to predict the gene clusters for antimicrobial substances identified a novel antimicrobial peptide cluster that belongs to the class I lantibiotic group. The predicted lantibiotic (homicorcin) was found to be 82% similar to a reported peptide epicidin 280 having a difference of seven amino acids at several positions of the core peptide. Two distinct peaks obtained at close retention times from a RP-HPLC purified fraction have comparable antimicrobial activities and LC–MS revealed the molecular mass of these peaks to be 3046.5 and 3043.2 Da. The presence of an oxidoreductase (homO) similar to that of epicidin 280- associated eciO or epilancin 15X- associated elxO in the homicorcin gene cluster is predicted to be responsible for the reduction of the first dehydrated residue dehydroalanine (Dha) to 2-hydroxypropionate that causes an increase of 3 Da mass of homicorcin 1. Trypsin digestion of the core peptide and its variant followed by ESI–MS analysis suggests the presence of three ring structures, one in the N-terminal and other two interlocking rings at the C-terminal region that remain undigested. Homicorcin exerts bactericidal activity against susceptible cells by disrupting the integrity of the cytoplasmic membrane through pore formation as observed under FE-SEM.

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Identification and Functional Analysis of ThADH1 and ThADH4 Genes Involved in Tolerance to Waterlogging Stress in Taxodium hybrid ‘Zhongshanshan 406’

Genes ◽

10.3390/genes12020225 ◽

2021 ◽

Vol 12 (2) ◽

pp. 225

Author(s):

Lei Xuan ◽

Jianfeng Hua ◽

Fan Zhang ◽

Zhiquan Wang ◽

Xiaoxiao Pei ◽

...

Keyword(s):

Ethanol Metabolism ◽

Flooding Tolerance ◽

Transcriptome Data ◽

Low Oxygen ◽

Anaerobic Conditions ◽

Waterlogging Tolerance ◽

Waterlogging Stress ◽

Adh Genes ◽

Oxygen Conditions ◽

Stems And Leaves

The Taxodium hybrid ‘Zhongshanshan 406’ (T. hybrid ‘Zhongshanshan 406’) [Taxodium mucronatum Tenore × Taxodium distichum (L.). Rich] has an outstanding advantage in flooding tolerance and thus has been widely used in wetland afforestation in China. Alcohol dehydrogenase genes (ADHs) played key roles in ethanol metabolism to maintain energy supply for plants in low-oxygen conditions. Two ADH genes were isolated and characterized—ThADH1 and ThADH4 (GenBank ID: AWL83216 and AWL83217—basing on the transcriptome data of T. hybrid ‘Zhongshanshan 406’ grown under waterlogging stress. Then the functions of these two genes were investigated through transient expression and overexpression. The results showed that the ThADH1 and ThADH4 proteins both fall under ADH III subfamily. ThADH1 was localized in the cytoplasm and nucleus, whereas ThADH4 was only localized in the cytoplasm. The expression of the two genes was stimulated by waterlogging and the expression level in roots was significantly higher than those in stems and leaves. The respective overexpression of ThADH1 and ThADH4 in Populus caused the opposite phenotype, while waterlogging tolerance of the two transgenic Populus significantly improved. Collectively, these results indicated that genes ThADH1 and ThADH4 were involved in the tolerance and adaptation to anaerobic conditions in T. hybrid ‘Zhongshanshan 406’.

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Analysis of municipal sewage pollution and denitrification treatment under low oxygen conditions

Environmental Technology & Innovation ◽

10.1016/j.eti.2020.101188 ◽

2020 ◽

pp. 101188

Author(s):

Fei Ye ◽

Jing Yan ◽

Ting Li

Keyword(s):

Municipal Sewage ◽

Low Oxygen ◽

Sewage Pollution ◽

Oxygen Conditions

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Complete Genome Sequence of Stenotrophomonas Phage Mendera

Microbiology Resource Announcements ◽

10.1128/mra.01411-19 ◽

2020 ◽

Vol 9 (1) ◽

Author(s):

Kameron D. Garza ◽

Heather Newkirk ◽

Russell Moreland ◽

Carlos F. Gonzalez ◽

Mei Liu ◽

...

Keyword(s):

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Stenotrophomonas Maltophilia ◽

Human Pathogen ◽

Base Pairs ◽

Content Type ◽

Genomic Annotation ◽

Opportunistic Human Pathogen

Stenotrophomonas maltophilia is an emerging opportunistic human pathogen. In this report, we describe the isolation and genomic annotation of the S. maltophilia-infecting bacteriophage Mendera. A myophage of 159,961 base pairs, Mendera is T4-like and related most closely to Stenotrophomonas phage IME-SM1.

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