scholarly journals Widespread Distribution and Functional Specificity of the Copper Importer CcoA: Distinct Cu Uptake Routes for Bacterial Cytochrome c Oxidases

mBio ◽  
2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Bahia Khalfaoui-Hassani ◽  
Hongjiang Wu ◽  
Crysten E. Blaby-Haas ◽  
Yang Zhang ◽  
Federica Sandri ◽  
...  
Keyword(s):  
Rhodobacter Capsulatus ◽  
Biochemical Characterization ◽  
Genomic Analysis ◽  
Primary Electron ◽  
Major Facilitator Superfamily ◽  
Close Relative ◽  
Comparative Genomic ◽  
Copper Uptake ◽  
Copper Trafficking ◽  
Copper Oxidase

ABSTRACT Cytochrome c oxidases are members of the heme-copper oxidase superfamily. These enzymes have different subunits, cofactors, and primary electron acceptors, yet they all contain identical heme-copper (CuB) binuclear centers within their catalytic subunits. The uptake and delivery pathways of the CuB atom incorporated into this active site, where oxygen is reduced to water, are not well understood. Our previous work with the facultative phototrophic bacterium Rhodobacter capsulatus indicated that the copper atom needed for the CuB site of cbb 3-type cytochrome c oxidase (cbb 3-Cox) is imported to the cytoplasm by a major facilitator superfamily-type transporter, CcoA. In this study, a comparative genomic analysis of CcoA orthologs in alphaproteobacterial genomes showed that CcoA is widespread among organisms and frequently co-occurs with cytochrome c oxidases. To define the specificity of CcoA activity, we investigated its function in Rhodobacter sphaeroides, a close relative of R. capsulatus that contains both cbb 3- and aa 3-Cox. Phenotypic, genetic, and biochemical characterization of mutants lacking CcoA showed that in its absence, or even in the presence of its bypass suppressors, only the production of cbb 3-Cox and not that of aa 3-Cox was affected. We therefore concluded that CcoA is dedicated solely to cbb 3-Cox biogenesis, establishing that distinct copper uptake systems provide the CuB atoms to the catalytic sites of these two similar cytochrome c oxidases. These findings illustrate the large variety of strategies that organisms employ to ensure homeostasis and fine control of copper trafficking and delivery to the target cuproproteins under different physiological conditions. IMPORTANCE The cbb 3- and aa 3-type cytochrome c oxidases belong to the widespread heme-copper oxidase superfamily. They are membrane-integral cuproproteins that catalyze oxygen reduction to water under hypoxic and normoxic growth conditions. These enzymes diverge in terms of subunit and cofactor composition, yet they all share a conserved heme-copper binuclear site within their catalytic subunit. In this study, we show that the copper atoms of the catalytic center of two similar cytochrome c oxidases from this superfamily are provided by different copper uptake systems during their biogenesis. This finding illustrates different strategies by which organisms fine-tune the trafficking of copper, which is an essential but toxic micronutrient.

scholarly journals Missense Mutations in CytochromecMaturation Genes Provide New Insights into Rhodobacter capsulatus cbb3-Type CytochromecOxidase Biogenesis

2012 ◽  
Vol 195 (2) ◽  
pp. 261-269 ◽  
Author(s):  
Seda Ekici ◽  
Xinpei Jiang ◽  
Hans-Georg Koch ◽  
Fevzi Daldal
Keyword(s):  
Rhodobacter Capsulatus ◽  
Major Facilitator Superfamily ◽  
Missense Mutations ◽  
Content Type ◽  
Knockout Mutants ◽  
Major Facilitator ◽  
Copper Oxidase ◽  
First Time ◽  
Derivatives Of

ABSTRACTTheRhodobacter capsulatus cbb3-type cytochromecoxidase (cbb3-Cox) belongs to the heme-copper oxidase superfamily, and its subunits are encoded by theccoNOQPoperon. Biosynthesis of this enzyme is complex and needs dedicated biogenesis genes (ccoGHIS). It also relies on thec-type cytochrome maturation (Ccm) process, which requires theccmABCDEFGHIgenes, because two of thecbb3-Cox subunits (CcoO and CcoP) arec-type cytochromes. Recently, we reported that mutants lacking CcoA, a major facilitator superfamily type transporter, produce very small amounts ofcbb3-Cox unless the growth medium is supplemented with copper. In this work, we isolated “Cu-unresponsive” derivatives of accoAdeletion strain that exhibited nocbb3-Cox activity even upon Cu supplementation. Molecular characterization of these mutants revealed missense mutations in theccmAorccmFgene, required for the Ccm process. As expected, Cu-unresponsive mutants lacked the CcoO and CcoP subunits due to Ccm defects, but remarkably, they contained the CcoN subunit ofcbb3-Cox. Subsequent construction and examination of singleccmknockout mutants demonstrated that membrane insertion and stability of CcoN occurred in the absence of the Ccm process. Moreover, while theccmknockout mutants were completely incompetent for photosynthesis, the Cu-unresponsive mutants grew photosynthetically at lower rates and produced smaller amounts of cytochromesc1andc2than did a wild-type strain due to their restricted Ccm capabilities. These findings demonstrate that different levels of Ccm efficiency are required for the production of variousc-type cytochromes and reveal for the first time that maturation of the heme-Cu-containing subunit CcoN ofR. capsulatus cbb3-Cox proceeds independently of that of thec-type cytochromes during the biogenesis of this enzyme.

scholarly journals Insights into algae evolution for adapting to blue-green light garnered from the Isochrysis galbana genome

2020 ◽  
Author(s):  
Duo Chen ◽  
Xue Yuan ◽  
Xuehai Zheng ◽  
Jingping Fang ◽  
Gang Lin ◽  
...  
Keyword(s):  
Metabolic Regulation ◽  
Green Light ◽  
Genomic Analysis ◽  
Isochrysis Galbana ◽  
Close Relative ◽  
Comparative Genomic ◽  
Evolutionary Analysis ◽  
Protein Coding ◽  
Domain Identification ◽  
Specific Complex

Isochrysis galbana is an important producer in the aquatic ecosystem because of its rich fucoxanthin content and fast growth. However, little is known about its evolutionary adaptation to live in a specific, complex and harsh environment. We report a high-quality genome sequence of I. galbana LG007, which has a 92.73 Mb genome size, a contig N50 of 6.99 Mb and 14,900 protein-coding genes. Phylogenomic inferences confirmed the monophyly of Haptophyta, showing I. galbana is a sister to E. huxleyi and C. tobinii. Evolutionary analysis revealed an estimated divergence of I. galbana from its close relative E. huxleyi ~133 million years ago, and I. galbana underwent one round of whole-genome duplication. Genes related to environmental adaptation and metabolic regulation in I. galbana were relatively conserved, but the basic transcriptional regulation toolkit for terrestrial plant development has been contracted or was not detected. The domain identification of one novel fucoxanthin biosynthesis gene that encodes diadinoxanthin-fucoxanthin hydroxylase (DFH) was investigated. Comparative genomic analysis revealed that I. galbana acquired several transcription factors specific to the control of pigment accumulation and production of LHCX2 to harvest blue-green light, which facilitates adaptation to the underwater environment. These findings provide new insights into the genomic characteristics of I. galbana and algae evolution for adaptation to blue-green light underwater.

scholarly journals Comparative Genomic Analysis of 450 Strains of Salmonella enterica Isolated from Diseased Animals

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1025
Author(s):  
Shaohua Zhao ◽  
Cong Li ◽  
Chih-Hao Hsu ◽  
Gregory H. Tyson ◽  
Errol Strain ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Bacterial Infections ◽  
Genomic Analysis ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Comparative Genomic ◽  
Salmonella Infections ◽  
Antimicrobial Resistance Genes ◽  
Salmonella Pathogenicity Islands ◽  
Shed Light

Salmonella is a leading cause of bacterial infections in animals and humans. We sequenced a collection of 450 Salmonella strains from diseased animals to better understand the genetic makeup of their virulence and resistance features. The presence of Salmonella pathogenicity islands (SPIs) varied by serotype. S. Enteritidis carried the most SPIs (n = 15), while S. Mbandaka, S. Cerro, S. Meleagridis, and S. Havana carried the least (n = 10). S. Typhimurium, S. Choleraesuis, S. I 4,5,12:i:-, and S. Enteritidis each contained the spv operon on IncFII or IncFII-IncFIB hybrid plasmids. Two S. IIIa carried a spv operon with spvD deletion on the chromosome. Twelve plasmid types including 24 hybrid plasmids were identified. IncA/C was frequently associated with S. Newport (83%) and S. Agona (100%) from bovine, whereas IncFII (100%), IncFIB (100%), and IncQ1 (94%) were seen in S. Choleraesuis from swine. IncX (100%) was detected in all S. Kentucky from chicken. A total of 60 antimicrobial resistance genes (ARGs), four disinfectant resistances genes (DRGs) and 33 heavy metal resistance genes (HMRGs) were identified. The Salmonella strains from sick animals contained various SPIs, resistance genes and plasmid types based on the serotype and source of the isolates. Such complicated genomic structures shed light on the strain characteristics contributing to the severity of disease and treatment failures in Salmonella infections, including those causing illnesses in animals.

scholarly journals Pathogenic Determinants of the Mycobacterium kansasii Complex: An Unsuspected Role for Distributive Conjugal Transfer

2021 ◽  
Vol 9 (2) ◽  
pp. 348
Author(s):  
Florian Tagini ◽  
Trestan Pillonel ◽  
Claire Bertelli ◽  
Katia Jaton ◽  
Gilbert Greub
Keyword(s):  
Genomic Analysis ◽  
Comparative Genomic ◽  
Mycobacterium Kansasii ◽  
Type Vii Secretion ◽  
A Genome ◽  
Genes Encoding ◽  
Associated Proteins ◽  
Immunosuppressed Patients ◽  
Type Vii Secretion System ◽  
Clinical Records

The Mycobacterium kansasii species comprises six subtypes that were recently classified into six closely related species; Mycobacterium kansasii (formerly M. kansasii subtype 1), Mycobacterium persicum (subtype 2), Mycobacterium pseudokansasii (subtype 3), Mycobacterium ostraviense (subtype 4), Mycobacterium innocens (subtype 5) and Mycobacterium attenuatum (subtype 6). Together with Mycobacterium gastri, they form the M. kansasii complex. M. kansasii is the most frequent and most pathogenic species of the complex. M. persicum is classically associated with diseases in immunosuppressed patients, and the other species are mostly colonizers, and are only very rarely reported in ill patients. Comparative genomics was used to assess the genetic determinants leading to the pathogenicity of members of the M. kansasii complex. The genomes of 51 isolates collected from patients with and without disease were sequenced and compared with 24 publicly available genomes. The pathogenicity of each isolate was determined based on the clinical records or public metadata. A comparative genomic analysis showed that all M. persicum, M. ostraviense, M innocens and M. gastri isolates lacked the ESX-1-associated EspACD locus that is thought to play a crucial role in the pathogenicity of M. tuberculosis and other non-tuberculous mycobacteria. Furthermore, M. kansasii was the only species exhibiting a 25-Kb-large genomic island encoding for 17 type-VII secretion system-associated proteins. Finally, a genome-wide association analysis revealed that two consecutive genes encoding a hemerythrin-like protein and a nitroreductase-like protein were significantly associated with pathogenicity. These two genes may be involved in the resistance to reactive oxygen and nitrogen species, a required mechanism for the intracellular survival of bacteria. Three non-pathogenic M. kansasii lacked these genes likely due to two distinct distributive conjugal transfers (DCTs) between M. attenuatum and M. kansasii, and one DCT between M. persicum and M. kansasii. To our knowledge, this is the first study linking DCT to reduced pathogenicity.

scholarly journals Comparative genomic analysis demonstrates that true reinfection following SARS-CoV-2 infection is possible

2021 ◽  
pp. 100015
Author(s):  
Eamon O. Murchu ◽  
Sinead O'Neill ◽  
Paula Byrne ◽  
Cillian De Gascun ◽  
Michelle O'Neill ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic
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