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Peng C, Wan X, Zhang J, Zhang B, Wang S, Ma T, Bian Y, Wang W. Bacterial diversity and competitors for degradation of hazardous oil refining waste under selective pressures of temperature and oxygen. J Hazard Mater 2022; 427:128201. [PMID: 34999399 DOI: 10.1016/j.jhazmat.2021.128201] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 12/28/2021] [Accepted: 12/30/2021] [Indexed: 02/08/2023]
Abstract
Oil refining waste (ORW) contains complex, hazardous, and refractory components, causing more severe long-term environmental pollution than petroleum. Here, ORW was used to simulate the accelerated domestication of bacteria from oily sludges and polymer-flooding wastewater, and the effects of key factors, oxygen and temperature, on the ORW degradation were evaluated. Bacterial communities acclimated respectively in 30/60 °C, aerobic/anaerobic conditions showed differentiated degradation rates of ORW, ranging from 5% to 34%. High-throughput amplicon sequencing and ORW component analysis revealed significant correlation between bacterial diversity/biomass and degradation efficiency/substrate preference. Under mesophilic and oxygen-rich condition, the high biomass and abundant biodiversity with diverse genes and pathways for petroleum hydrocarbons degradation, effectively promoted the rapid and multi-component degradation of ORW. While under harsh conditions, a few dominant genera still contributed to ORW degradation, although the biodiversity was severely restricted. The typical dominant facultative anaerobes Bacillus (up to 99.8% abundance anaerobically) and Geobacillus (up to 99.9% abundance aerobically and anaerobically) showed oxygen-independent sustainable degradation ability and broad-spectrum of temperature adaptability, making them promising and competitive bioremediation candidates for future application. Our findings provide important strategies for practical bioremediation of varied environments polluted by hazardous ORW.
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2
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Sun S, Song X, Bian Y, Wan X, Zhang J, Wang W. Multi-parameter optimization maximizes the performance of genetically engineered Geobacillus for degradation of high-concentration nitroalkanes in wastewater. Bioresour Technol 2022; 347:126690. [PMID: 35007737 DOI: 10.1016/j.biortech.2022.126690] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/02/2022] [Accepted: 01/05/2022] [Indexed: 02/08/2023]
Abstract
Nitroalkanes are important toxic pollutants for which there is no effective removal method at present. Although genetic engineering bacteria have been developed as a promising bioremediation strategy for years, their actual performance is far lower than expected. In this study, important factors affecting the application of engineered Geobacillus for nitroalkanes degradation were comprehensively optimized. The deep-reconstructed engineered strains significantly raised the expression and activity level of catalytic enzymes, but failed to fully enhance the degradation efficiency. However, further debugging of a variety of key parameters effectively improved the performance of the engineering strains. The increased cell membrane permeability, trace supplementation of vital nutritional factors, synergy of multifunctional enzyme engineered bacteria, switch of oxygen-supply mode, and moderate initial biomass all effectively boosted the degradation efficiency. Finally, a low-cost and highly effective bioreactor test for high-concentration nitroalkanes degradation proved the multi-parameter optimization mode helps to maximize the performance of genetically engineered bacteria.
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Affiliation(s)
- Shenmei Sun
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China
| | - Xiaoru Song
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China
| | - Ya Bian
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China
| | - Xuehua Wan
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China
| | - Jingjing Zhang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China
| | - Wei Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China; Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin 300457, PR China.
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3
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Wan X, Saito JA, Hou S, Geib SM, Yuryev A, Higa LM, Womersley CZ, Alam M. Author Correction: The Aphelenchus avenae genome highlights evolutionary adaptation to desiccation. Commun Biol 2021; 4:1299. [PMID: 34773097 DOI: 10.1038/s42003-021-02824-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
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Wan X, Saito JA, Hou S, Geib SM, Yuryev A, Higa LM, Womersley CZ, Alam M. The Aphelenchus avenae genome highlights evolutionary adaptation to desiccation. Commun Biol 2021; 4:1232. [PMID: 34711923 PMCID: PMC8553787 DOI: 10.1038/s42003-021-02778-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 10/09/2021] [Indexed: 02/08/2023] Open
Abstract
Some organisms can withstand complete body water loss (losing up to 99% of body water) and stay in ametabolic state for decades until rehydration, which is known as anhydrobiosis. Few multicellular eukaryotes on their adult stage can withstand life without water. We still have an incomplete understanding of the mechanism for metazoan survival of anhydrobiosis. Here we report the 255-Mb genome of Aphelenchus avenae, which can endure relative zero humidity for years. Gene duplications arose genome-wide and contributed to the expansion and diversification of 763 kinases, which represents the second largest metazoan kinome to date. Transcriptome analyses of ametabolic state of A. avenae indicate the elevation of ATP level for global recycling of macromolecules and enhancement of autophagy in the early stage of anhydrobiosis. We catalogue 74 species-specific intrinsically disordered proteins, which may facilitate A. avenae to survive through desiccation stress. Our findings refine a molecular basis evolving for survival in extreme water loss and open the way for discovering new anti-desiccation strategies. Wan et al. report the genome and transcriptome of the Aphelenchus avenae nematode that can withstand long-term extreme desiccation. This study compares gene features to eight other nematode species and identifies intrinsically disordered proteins and changes in gene expression that contribute toward anhydrobiosis adaptation.
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Affiliation(s)
- Xuehua Wan
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, HI, USA. .,TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China.
| | - Jennifer A Saito
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, HI, USA
| | - Shaobin Hou
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, HI, USA
| | - Scott M Geib
- Tropical Crop and Commodity Protection Research Unit, USDA-ARS Pacific Basin Agricultural Research Center, Hilo, HI, USA
| | - Anton Yuryev
- Elsevier Life Sciences Solutions, Rockville, MD, USA
| | - Lynne M Higa
- School of Life Sciences, University of Hawaii, Honolulu, HI, USA
| | | | - Maqsudul Alam
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, HI, USA
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5
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Zhang M, Lv Y, Hou S, Liu Y, Wang Y, Wan X. Differential Mucosal Microbiome Profiles across Stages of Human Colorectal Cancer. Life (Basel). 2021;11. [PMID: 34440574 DOI: 10.3390/Life11080831] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/12/2021] [Accepted: 08/12/2021] [Indexed: 02/06/2023] Open
Abstract
Emerging evidences link gut microbiota to colorectal cancer (CRC) initiation and development. However, the CRC stage- and spatial-specific bacterial taxa were less investigated, especially in a Chinese cohort, leading to our incomplete understanding of the functional roles of gut microbiota in promoting CRC progression and recurrence. Here, we report the composition and structure of gut microbiota across CRC stages I, II and III, by analyzing the gut mucosal microbiomes of 75 triplet-paired samples collected from on-tumor, adjacent-tumor and off-tumor sites and 26 healthy controls. We observed tumor-specific pattern of mucosal microbiome profiles as CRC progressed and identified ten bacterial taxa with high abundances (>1%) as potential biomarkers for tumor initiation and development. Peptostreptococcus and Parvimonas can serve as biomarkers for CRC stage I. Fusobacterium, Streptococcus, Parvimonas, Burkholderiales, Caulobacteraceae, Delftia and Oxalobacteraceae can serve as biomarkers for CRC stage II, while Fusobacterium, Burkholderiales, Caulobacteraceae, Oxalobacteraceae, Faecalibacterium and Sutterella can serve as biomarkers for CRC stage III. These biomarkers classified CRC stages I, II and III distinguished from each other with an area under the receiver-operating curve (AUC) > 0.5. Moreover, co-occurrence and co-excluding network analysis of these genera showed strong correlations in CRC stage I, which were subsequently reduced in CRC stages II and III. Our findings provide a reference index for stage-specific CRC diagnosis and suggest stage-specific roles of Peptostreptococcus, Fusobacterium, Streptococcus and Parvimonas in driving CRC progression.
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Abstract
Background Inflammatory bowel disease caused by microbial dysbiosis is an important factor contributing to colorectal cancer (CRC) initiation. The ‘driver-passenger’ model in human gut microbial dysbiosis suggests that ‘driver’ bacteria may colonize with low relative abundance on tumor site but persistently induce chronic change in normal intestinal epithelium and initiate CRC. They are gradually replaced by ‘passenger’ bacteria later on, due to their low adaptability to the on-tumor site niche. Results To reveal site-specific bacterial taxon markers in CRC patients, we analyzed the gut mucosal microbiome of 75 paired samples of on-tumor and tumor-adjacent sites, 75 off-tumor sites, and 26 healthy controls. Linear discriminant analysis of relative abundance profiles revealed unique bacterial taxon distribution correlated with specific tumor sites, with Eubacterium having the distribution characteristic of potential driver bacteria. We further show that Eubacterium rectale endotoxin activates the transcription factor NF-κΒ, which regulates multiple aspects of innate and adaptive immune responses in normal colon epithelial cells. Unlike the ‘passenger’ bacterium Fusobacterium nucleatum, E. rectale promotes dextran sodium sulfate-induced colitis in Balb/c mice. Conclusions Our findings reveal that E. rectale functions as a ‘driver’ bacterium and contributes to cancer initiation via promoting inflammation.
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Affiliation(s)
- Yijia Wang
- Laboratory of Oncologic Molecular Medicine, Tianjin Union Medical Center, Nankai University, No. 190 Jieyuan Rd., Hongqiao district, Tianjin, 300121, China
| | - Xuehua Wan
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300071, China
| | - Xiaojing Wu
- Laboratory of Oncologic Molecular Medicine, Tianjin Union Medical Center, Nankai University, No. 190 Jieyuan Rd., Hongqiao district, Tianjin, 300121, China
| | - Chunze Zhang
- Laboratory of Oncologic Molecular Medicine, Tianjin Union Medical Center, Nankai University, No. 190 Jieyuan Rd., Hongqiao district, Tianjin, 300121, China
| | - Jun Liu
- Laboratory of Oncologic Molecular Medicine, Tianjin Union Medical Center, Nankai University, No. 190 Jieyuan Rd., Hongqiao district, Tianjin, 300121, China.
| | - Shaobin Hou
- Advanced Studies in Genomics, Proteomics, and Bioinformatics, University of Hawaii At Manoa, 2538 McCarthy Mall, Snyder Hall, Honolulu, HI, 96822, USA.
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Sun H, Song Y, Chen F, Zhou C, Liu P, Fan Y, Zheng Y, Wan X, Feng L. An ArcA-Modulated Small RNA in Pathogenic Escherichia coli K1. Front Microbiol 2020; 11:574833. [PMID: 33329434 PMCID: PMC7719688 DOI: 10.3389/fmicb.2020.574833] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 10/23/2020] [Indexed: 02/05/2023] Open
Abstract
Escherichia coli K1 is the leading cause of meningitis in newborns. Understanding the molecular basis of E. coli K1 pathogenicity will help develop treatment of meningitis and prevent neurological sequelae. E. coli K1 replicates in host blood and forms a high level of bacteremia to cause meningitis in human. However, the mechanisms that E. coli K1 employs to sense niche signals for survival in host blood are poorly understood. We identified one intergenic region in E. coli K1 genome that encodes a novel small RNA, sRNA-17. The expression of sRNA-17 was downregulated by ArcA in microaerophilic blood. The ΔsRNA-17 strain grew better in blood than did the wild-type strain and enhanced invasion frequency in human brain microvascular endothelial cells. Transcriptome analyses revealed that sRNA-17 regulates tens of differentially expressed genes. These data indicate that ArcA downregulates the sRNA-17 expression to benefit bacterial survival in blood and penetration of the blood–brain barrier. Our findings reveal a signaling mechanism in E. coli K1 for host adaptation.
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Affiliation(s)
- Hao Sun
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China.,College of Life Sciences, Nankai University, Tianjin, China
| | - Yajun Song
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China.,College of Life Sciences, Nankai University, Tianjin, China
| | - Fang Chen
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China
| | - Changhong Zhou
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China
| | - Peng Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China
| | - Yu Fan
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China
| | - Yangyang Zheng
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China.,College of Life Sciences, Nankai University, Tianjin, China
| | - Xuehua Wan
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China
| | - Lu Feng
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China.,College of Life Sciences, Nankai University, Tianjin, China
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8
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Wang Y, Zhang C, Hou S, Wu X, Liu J, Wan X. Analyses of Potential Driver and Passenger Bacteria in Human Colorectal Cancer. Cancer Manag Res 2020; 12:11553-11561. [PMID: 33209059 PMCID: PMC7669530 DOI: 10.2147/cmar.s275316] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/25/2020] [Indexed: 02/05/2023] Open
Abstract
Introduction Besides genetic and epigenetic alterations that lead to carcinogenesis and development of colorectal cancer (CRC), intestinal microbiomes are recently recognized to play a critical role in CRC progression. The abundant species associated with human CRC have been proposed for their roles in promoting tumorigenesis. However, a recent “driver-passenger” model suggests that these CRC-associated species with high relative abundances may be passenger bacteria that take advantage of the tumor environment instead of initiating CRC, whereas the driver species that initiate CRC have been replaced by passenger bacteria due to the alteration of the intestinal niche. Methods Here, to reveal potential driver and passenger bacteria during CRC progression, we compare the gut mucosal microbiomes of 75 triplet-paired CRC samples collected from on-tumor site, adjacent-tumor site, and off-tumor site, and 26 healthy controls. Results Our analyses revealed potential driver bacteria in four genera and two families, and potential passenger bacteria in 14 genera or families. Bacillus, Bradyrhizobium, Methylobacterium, Streptomyces, Intrasporangiaceae and Sinobacteraceae were predicted to be potential driver bacteria. Moreover, 14 potential passenger bacteria were identified and divided into five groups. Group I passenger bacteria contain Fusobacterium, Campylobacter, Streptococcus, Schwartzia, and Parvimonas. Group II passenger bacteria contain Dethiosulfatibacter, Selenomonas, Peptostreptococus, Leptotrichia. Group III passenger bacteria contain Granulicatella. Group IV passenger bacteria contain Shewanella, Mogibacterium, and Eikenella. Group V passenger bacteria contain Anaerococus. Co-occurrence network analysis reveals a low correlation relationship between driver and passenger bacteria in CRC patients compared with healthy controls. Discussion These driver and passenger species may serve as bio-marker species for screening cohorts with high risk to initiate CRC or patients with CRC, respectively. Further functional studies will help understand the roles of driver and passenger bacteria in CRC initiation and development.
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Affiliation(s)
- Yijia Wang
- Laboratory of Oncologic Molecular Medicine, Tianjin Union Medical Center, Nankai University, Tianjin, People's Republic of China
| | - Chunze Zhang
- Department of Colorectal Surgery, Tianjin Union Medical Center, Nankai University, Tianjin, People's Republic of China
| | - Shaobin Hou
- Advanced Studies in Genomics, Proteomics, and Bioinformatics, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Xiaojing Wu
- Laboratory of Oncologic Molecular Medicine, Tianjin Union Medical Center, Nankai University, Tianjin, People's Republic of China
| | - Jun Liu
- Department of Radiology, Tianjin Union Medical Center, Nankai University, Tianjin, People's Republic of China
| | - Xuehua Wan
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
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Wan X. Comparative Genome Analyses Reveal the Genomic Traits and Host Plant Adaptations of Flavobacterium akiainvivens IK-1 T. Int J Mol Sci 2019; 20:ijms20194910. [PMID: 31623351 PMCID: PMC6801697 DOI: 10.3390/ijms20194910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/24/2019] [Accepted: 10/02/2019] [Indexed: 02/05/2023] Open
Abstract
The genus Flavobacterium contains a large group of commensal bacteria identified in diverse terrestrial and aquatic habitats. We compared the genome of a new species Flavobacterium akiainvivens IK-1T to public available genomes of Flavobacterium species to reveal the genomic traits and ecological roles of IK-1T. Principle component analysis (PCA) of carbohydrate-active enzyme classes suggests that IK-1T belongs to a terrestrial clade of Flavobacterium. In addition, type 2 and type 9 secretion systems involved in bacteria-environment interactions were identified in the IK-1T genome. The IK-1T genome encodes eukaryotic-like domain containing proteins including ankyrin repeats, von Willebrand factor type A domain, and major royal jelly proteins, suggesting that IK-1T may alter plant host physiology by secreting eukaryotic-like proteins that mimic host proteins. A novel two-component system FaRpfC-FaYpdB was identified in the IK-1T genome, which may mediate quorum sensing to regulate global gene expressions. Our findings suggest that comparative genome analyses of Flavobacterium spp. reveal that IK-1T has adapted to a terrestrial niche. Further functional characterizations of IK-1T secreted proteins and their regulation systems will shed light on molecular basis of bacteria-plant interactions in environments.
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Affiliation(s)
- Xuehua Wan
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300071, China.
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300071, China.
- Tianjin Key Laboratory of Microbial Functional Genomics, Nankai University, Tianjin 300071, China.
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Koster KJ, Largen A, Foster JT, Drees KP, Qian L, Desmond E, Wan X, Hou S, Douglas JT. Genomic sequencing is required for identification of tuberculosis transmission in Hawaii. BMC Infect Dis 2018; 18:608. [PMID: 30509214 PMCID: PMC6276198 DOI: 10.1186/s12879-018-3502-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 11/02/2018] [Indexed: 02/08/2023] Open
Abstract
Background Tuberculosis (TB) caused an estimated 1.4 million deaths and 10.4 million new cases globally in 2015. TB rates in the United States continue to steadily decline, yet rates in the State of Hawaii are perennially among the highest in the nation due to a continuous influx of immigrants from the Western Pacific and Asia. TB in Hawaii is composed of a unique distribution of genetic lineages, with the Beijing and Manila families of Mycobacterium tuberculosis (Mtb) comprising over two-thirds of TB cases. Standard fingerprinting methods (spoligotyping plus 24-loci Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeats [MIRU-VNTR] fingerprinting) perform poorly when used to identify actual transmission clusters composed of isolates from these two families. Those typing methods typically group isolates from these families into large clusters of non-linked isolates with identical fingerprints. Next-generation whole-genome sequencing (WGS) provides a new tool for molecular epidemiology that can resolve clusters of isolates with identical spoligotyping and MIRU-VNTR fingerprints. Methods We performed WGS and SNP analysis and evaluated epidemiological data to investigate 19 apparent TB transmission clusters in Hawaii from 2003 to 2017 in order to assess WGS’ ability to resolve putative Mtb clusters from the Beijing and Manila families. This project additionally investigated MIRU-VNTR allele prevalence to determine why standard Mtb fingerprinting fails to usefully distinguish actual transmission clusters from these two Mtb families. Results WGS excluded transmission events in seven of these putative clusters, confirmed transmission in eight, and identified both transmission-linked and non-linked isolates in four. For epidemiologically identified clusters, while the sensitivity of MIRU-VNTR fingerprinting for identifying actual transmission clusters was found to be 100%, its specificity was only 28.6% relative to WGS. We identified that the Beijing and Manila families’ significantly lower Shannon evenness of MIRU-VNTR allele distributions than lineage 4 was the cause of standard fingerprinting’s poor performance when identifying transmission in Beijing and Manila family clusters. Conclusions This study demonstrated that WGS is necessary for epidemiological investigation of TB in Hawaii and the Pacific. Electronic supplementary material The online version of this article (10.1186/s12879-018-3502-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Angela Largen
- Hawaii State Department of Health, Honolulu, HI, USA
| | - Jeffrey T Foster
- University of New Hampshire, Durham, NH, USA.,Present Address: Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Lishi Qian
- University of Hawaii at Manoa, Honolulu, HI, USA
| | - Ed Desmond
- California Department of Public Health, Richmond, CA, USA
| | - Xuehua Wan
- Advanced Studies in Genomics, Proteomics and Bioinformatics, Honolulu, HI, USA
| | - Shaobin Hou
- Advanced Studies in Genomics, Proteomics and Bioinformatics, Honolulu, HI, USA
| | - James T Douglas
- University of Hawaii at Manoa, Honolulu, HI, USA. .,Present Address: Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
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Koster K, Largen A, Foster JT, Drees KP, Qian L, Desmond EP, Wan X, Hou S, Douglas JT. Whole genome SNP analysis suggests unique virulence factor differences of the Beijing and Manila families of Mycobacterium tuberculosis found in Hawaii. PLoS One 2018; 13:e0201146. [PMID: 30036392 PMCID: PMC6056056 DOI: 10.1371/journal.pone.0201146] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 07/09/2018] [Indexed: 02/05/2023] Open
Abstract
While tuberculosis (TB) remains a global disease, the WHO estimates that 62% of the incident TB cases in 2016 occurred in the WHO South-East Asia and Western Pacific regions. TB in the Pacific is composed predominantly of two genetic families of Mycobacterium tuberculosis (Mtb): Beijing and Manila. The Manila family is historically under-studied relative to the families that comprise the majority of TB in Europe and North America (e.g. lineage 4), and it remains unclear why this lineage has persisted in Filipino populations despite the predominance of more globally successful Mtb lineages in most of the world. The Beijing family is of particular interest as it is increasingly associated with drug resistance throughout the world. Both of these lineages are important to the State of Hawaii, where they comprise over two-thirds of TB cases. Here, we performed whole genome sequencing on 82 Beijing family, Manila family, and outgroup clinical Mtb isolates from Hawaii to identify lineage-specific SNPs (SNPs found in all isolates from their respective families, and exclusively in those families) in established virulence factor genes. Six non-silent lineage-specific virulence factor SNPs were found in the Beijing family, including mutations in alternative sigma factor sigG and polyketide synthases pks5 and pks7. The Manila family displayed more than eleven non-silent lineage-specific and characteristic virulence factor mutations, including in genes coding for MCE-family protein Mce1B, two mutations in fatty-acid-AMP ligase FadD26, and virulence-regulating transcriptional regulator VirS. This study further identified an ancient clade that shared some virulence factor mutations with the Manila family, and investigated the relationship of those and other “Manila-like” spoligotypes to the Manila family with this SNP dataset. This work identified a set of virulence genes that are worth pursuing to determine potential differences in transmission or virulence displayed by these two Mtb families.
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Affiliation(s)
- Kent Koster
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Angela Largen
- Hawaii State Department of Health, Honolulu, Hawaii, United States of America
| | - Jeffrey T. Foster
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Kevin P. Drees
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, United States of America
| | - Lishi Qian
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Edward P. Desmond
- California Department of Public Health, Richmond, California, United States of America
| | - Xuehua Wan
- Advanced Studies in Genomics, Proteomics and Bioinformatics, Honolulu, Hawaii, United States of America
| | - Shaobin Hou
- Advanced Studies in Genomics, Proteomics and Bioinformatics, Honolulu, Hawaii, United States of America
| | - James T. Douglas
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
- * E-mail:
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Hayashi K, Busse HJ, Golke J, Anderson J, Wan X, Hou S, Chain PSG, Prescott RD, Donachie SP. Rheinheimera salexigens sp. nov., isolated from a fishing hook, and emended description of the genus Rheinheimera. Int J Syst Evol Microbiol 2017; 68:35-41. [PMID: 29111971 DOI: 10.1099/ijsem.0.002412] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A Gram-negative, rod-shaped bacterium, designated KH87T, was isolated from a fishing hook that had been baited and suspended in seawater off O'ahu, Hawai'i. Based on a comparison of 1524 nt of the 16S rRNA gene sequence of strain KH87T, its nearest neighbours were the GammaproteobacteriaRheinheimera nanhaiensis E407-8T (96.2 % identity), Rheinheimera chironomi K19414T (96.0 %), Rheinheimera pacifica KMM 1406T (95.8 %), Rheinheimera muenzenbergensis E49T (95.7 %), Alishewanella solinquinati KMK6T (94.9 %) and Arsukibacterium ikkense GCM72T (94.6 %). Cells of KH87T were motile by a single polar flagellum, strictly aerobic, and catalase- and oxidase-positive. Growth occurred between 4 and 39 °C, and in a circumneutral pH range. Major fatty acids in whole cells of strain KH87T were cis-9-hexadecenoic acid, hexadecanoic acid and cis-11-octadecenoic acid. The quinone system contained mostly menaquinone MK-7, and a minor amount of ubiquinone Q-8. The polar lipid profile contained the major lipids phosphatidylglycerol, phosphatidylserine, phosphatidylethanolamine, an unidentified aminolipid, and a lipid not containing phosphate, an amino group or a sugar moiety. Putrescine was the major polyamine. Physiological, biochemical and genomic data, including obligate halophily, absence of amylolytic activity, a quinone system dominated by MK-7 and DNA G+C content (42.0 mol%) distinguished KH87T from extant Rheinheimera species; strain KH87T was also distinguished by a multi-locus sequence analysis of aligned and concatenated 16S rRNA, gyrB, rpoB and rpoD gene sequences. Based on phenotypic and genotypic differences, the species Rheinheimera salexigens sp. nov. is proposed to accommodate KH87T as the type strain (=ATCC BAA-2715T=CIP 111115T). An emended description of the genus Rheinheimera is also proposed.
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Affiliation(s)
- Kazukuni Hayashi
- Department of Microbiology, University of Hawai'i at Mānoa, Snyder Hall, 2538 McCarthy Mall, Honolulu, HI 96822, USA
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Wien, Austria
| | - Jan Golke
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Wien, Austria
| | - James Anderson
- The Hawai'i Institute of Marine Biology, 46-007 Lilipuna Road, Kane'ohe, HI 96744, USA
- Department of Biology, University of Hawai'i at Mānoa, Edmondson Hall, 2538 McCarthy Mall, Honolulu, HI 96822, USA
| | - Xuehua Wan
- Department of Microbiology, University of Hawai'i at Mānoa, Snyder Hall, 2538 McCarthy Mall, Honolulu, HI 96822, USA
- Advanced Studies in Genomics, Proteomics, and Bioinformatics, University of Hawai'i at Mānoa, Snyder Hall, 2538 McCarthy Mall, Honolulu, HI 96822, USA
| | - Shaobin Hou
- Department of Microbiology, University of Hawai'i at Mānoa, Snyder Hall, 2538 McCarthy Mall, Honolulu, HI 96822, USA
- Advanced Studies in Genomics, Proteomics, and Bioinformatics, University of Hawai'i at Mānoa, Snyder Hall, 2538 McCarthy Mall, Honolulu, HI 96822, USA
| | - Patrick S G Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Rebecca D Prescott
- Department of Microbiology, University of Hawai'i at Mānoa, Snyder Hall, 2538 McCarthy Mall, Honolulu, HI 96822, USA
| | - Stuart P Donachie
- Advanced Studies in Genomics, Proteomics, and Bioinformatics, University of Hawai'i at Mānoa, Snyder Hall, 2538 McCarthy Mall, Honolulu, HI 96822, USA
- Department of Microbiology, University of Hawai'i at Mānoa, Snyder Hall, 2538 McCarthy Mall, Honolulu, HI 96822, USA
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13
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Wan X, Darris M, Hou S, Donachie SP. Draft Genome Sequence of a Novel Chitinophaga sp. Strain, MD30, Isolated from a Biofilm in an Air Conditioner Condensate Pipe. Genome Announc 2017; 5:e01161-17. [PMID: 29051259 DOI: 10.1128/genomeA.01161-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Most of the 24 known Chitinophaga species were originally isolated from soils. We report the draft genome sequence of a putatively novel Chitinophaga sp. from a biofilm in an air conditioner condensate pipe. The genome comprises 7,661,303 bp in one scaffold, 5,694 predicted protein-coding sequences, and a G+C content of 47.6%.
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14
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Wan X, Saito JA, Newhouse JS, Hou S, Alam M. The importance of conserved amino acids in heme-based globin-coupled diguanylate cyclases. PLoS One 2017; 12:e0182782. [PMID: 28792538 PMCID: PMC5549716 DOI: 10.1371/journal.pone.0182782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/24/2017] [Indexed: 02/05/2023] Open
Abstract
Globin-coupled diguanylate cyclases contain globin, middle, and diguanylate cyclase domains that sense O2 to synthesize c-di-GMP and regulate bacterial motility, biofilm formation, and virulence. However, relatively few studies have extensively examined the roles of individual residues and domains of globin-coupled diguanylate cyclases, which can shed light on their signaling mechanisms and provide drug targets. Here, we report the critical residues of two globin-coupled diguanylate cyclases, EcGReg from Escherichia coli and BpeGReg from Bordetella pertussis, and show that their diguanylate cyclase activity requires an intact globin domain. In the distal heme pocket of the globin domain, residues Phe42, Tyr43, Ala68 (EcGReg)/Ser68 (BpeGReg), and Met69 are required to maintain full diguanylate cyclase activity. The highly conserved amino acids His223/His225 and Lys224/Lys226 in the middle domain of EcGReg/BpeGReg are essential to diguanylate cyclase activity. We also identified sixteen important residues (Leu300, Arg306, Asp333, Phe337, Lys338, Asn341, Asp342, Asp350, Leu353, Asp368, Arg372, Gly374, Gly375, Asp376, Glu377, and Phe378) in the active site and inhibitory site of the diguanylate cyclase domain of EcGReg. Moreover, BpeGReg266 (residues 1–266) and BpeGReg296 (residues 1–296), which only contain the globin and middle domains, can inhibit bacterial motility. Our findings suggest that the distal residues of the globin domain affect diguanylate cyclase activity and that BpeGReg may interact with other c-di-GMP-metabolizing proteins to form mixed signaling teams.
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Affiliation(s)
- Xuehua Wan
- Department of Microbiology, University of Hawaii, Honolulu, Hawaii, United States of America
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii, United States of America
- * E-mail:
| | - Jennifer A. Saito
- Department of Microbiology, University of Hawaii, Honolulu, Hawaii, United States of America
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii, United States of America
| | - James S. Newhouse
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Shaobin Hou
- Department of Microbiology, University of Hawaii, Honolulu, Hawaii, United States of America
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Maqsudul Alam
- Department of Microbiology, University of Hawaii, Honolulu, Hawaii, United States of America
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii, United States of America
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15
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Wan X, Koster K, Qian L, Desmond E, Brostrom R, Hou S, Douglas JT. Genomic analyses of the ancestral Manila family of Mycobacterium tuberculosis. PLoS One 2017; 12:e0175330. [PMID: 28394899 PMCID: PMC5386241 DOI: 10.1371/journal.pone.0175330] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/25/2017] [Indexed: 02/05/2023] Open
Abstract
With its airborne transmission and prolonged latency period, Mycobacterium tuberculosis spreads worldwide as one of the most successful bacterial pathogens and continues to kill millions of people every year. M. tuberculosis lineage 1 is inferred to originate ancestrally based on the presence of the 52-bp TbD1 sequence and analysis of single nucleotide polymorphisms. Previously, we briefly reported the complete genome sequencing of M. tuberculosis strains 96121 and 96075, which belong to the ancient Manila family and modern Beijing family respectively. Here we present the comprehensive genomic analyses of the Manila family in lineage 1 compared to complete genomes in lineages 2-4. Principal component analysis of the presence and absence of CRISPR spacers suggests that Manila isolate 96121 is distinctly distant from lineages 2-4. We further identify a truncated whiB5 gene and a putative operon consisting of genes encoding a putative serine/threonine kinase PknH and a putative ABC transporter, which are only found in the genomes of Manila family isolates. Six single nucleotide polymorphisms are uniquely conserved in 38 Manila strains. Moreover, when compared to M. tuberculosis H37Rv, 59 proteins are under positive selection in Manila family isolate 96121 but not in Beijing family isolate 96075. The unique features further serve as biomarkers for Manila strains and may shed light on the limited transmission of this ancestral lineage outside of its Filipino host population.
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Affiliation(s)
- Xuehua Wan
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Kent Koster
- Department of Microbiology, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Lishi Qian
- Department of Microbiology, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Edward Desmond
- Microbial Diseases Laboratory, California Department of Public Health, Richmond, California, United States of America
| | - Richard Brostrom
- TB Control Program, Hawaii State Department of Health, Honolulu, Hawaii, United States of America
| | - Shaobin Hou
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii, United States of America
| | - James T. Douglas
- Department of Microbiology, University of Hawaii, Honolulu, Hawaii, United States of America
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16
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Islam MS, Saito JA, Emdad EM, Ahmed B, Islam MM, Halim A, Hossen QMM, Hossain MZ, Ahmed R, Hossain MS, Kabir SMT, Khan MSA, Khan MM, Hasan R, Aktar N, Honi U, Islam R, Rashid MM, Wan X, Hou S, Haque T, Azam MS, Moosa MM, Elias SM, Hasan AMM, Mahmood N, Shafiuddin M, Shahid S, Shommu NS, Jahan S, Roy S, Chowdhury A, Akhand AI, Nisho GM, Uddin KS, Rabeya T, Hoque SME, Snigdha AR, Mortoza S, Matin SA, Islam MK, Lashkar MZH, Zaman M, Yuryev A, Uddin MK, Rahman MS, Haque MS, Alam MM, Khan H, Alam M. Comparative genomics of two jute species and insight into fibre biogenesis. Nat Plants 2017; 3:16223. [PMID: 28134914 DOI: 10.1038/nplants.2016.223] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 12/21/2016] [Indexed: 02/08/2023]
Abstract
Jute (Corchorus sp.) is one of the most important sources of natural fibre, covering ∼80% of global bast fibre production1. Only Corchorus olitorius and Corchorus capsularis are commercially cultivated, though there are more than 100 Corchorus species2 in the Malvaceae family. Here we describe high-quality draft genomes of these two species and their comparisons at the functional genomics level to support tailor-designed breeding. The assemblies cover 91.6% and 82.2% of the estimated genome sizes for C. olitorius and C. capsularis, respectively. In total, 37,031 C. olitorius and 30,096 C. capsularis genes are identified, and most of the genes are validated by cDNA and RNA-seq data. Analyses of clustered gene families and gene collinearity show that jute underwent shared whole-genome duplication ∼18.66 million years (Myr) ago prior to speciation. RNA expression analysis from isolated fibre cells reveals the key regulatory and structural genes involved in fibre formation. This work expands our understanding of the molecular basis of fibre formation laying the foundation for the genetic improvement of jute.
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Affiliation(s)
- Md Shahidul Islam
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Jennifer A Saito
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii 96822, USA
| | - Emdadul Mannan Emdad
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Borhan Ahmed
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Mohammad Moinul Islam
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Abdul Halim
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Quazi Md Mosaddeque Hossen
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Md Zakir Hossain
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Rasel Ahmed
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Md Sabbir Hossain
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Shah Md Tamim Kabir
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Md Sarwar Alam Khan
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Md Mursalin Khan
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Rajnee Hasan
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Nasima Aktar
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Ummay Honi
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Rahin Islam
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Md Mamunur Rashid
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Xuehua Wan
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii 96822, USA
| | - Shaobin Hou
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii 96822, USA
| | - Taslima Haque
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | | | | | - Sabrina M Elias
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - A M Mahedi Hasan
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Niaz Mahmood
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Md Shafiuddin
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Saima Shahid
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | | | - Sharmin Jahan
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Saroj Roy
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh
| | - Amlan Chowdhury
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh
| | - Ashikul Islam Akhand
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh
| | - Golam Morshad Nisho
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh
| | - Khaled Salah Uddin
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh
| | - Taposhi Rabeya
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh
| | - S M Ekramul Hoque
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh
| | - Afsana Rahman Snigdha
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh
| | - Sarowar Mortoza
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh
| | - Syed Abdul Matin
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh
| | - Md Kamrul Islam
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh
| | - M Z H Lashkar
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh
| | - Mahboob Zaman
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh
| | - Anton Yuryev
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Elsevier, Rockville, Maryland, Missouri 63043, USA
| | - Md Kamal Uddin
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Md Sharifur Rahman
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Department of Telecommunications, Dhaka 1208, Bangladesh
| | - Md Samiul Haque
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Md Monjurul Alam
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Haseena Khan
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Maqsudul Alam
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii 96822, USA
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17
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Wan X, Hou S, Hayashi K, Anderson J, Donachie SP. Genome Sequence of Rheinheimera salexigens sp. nov. Isolated from a Fishing Hook off O'ahu, Hawai'i. Genome Announc 2016; 4:e01390-16. [PMID: 27979942 DOI: 10.1128/genomeA.01390-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Rheinheimera salexigens KH87T is an obligately halophilic gammaproteobacterium. The strain’s draft genome sequence, generated by the Roche 454 GS FLX+ platform, comprises two scaffolds of ~3.4 Mbp and ~3 kbp, with 3,030 protein-coding sequences and 58 tRNA coding regions. The G+C content is 42 mol%.
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18
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Wan X, Hou S, Burns SL, Saito JA, Donachie SP. Draft Genome Sequence of a Novel Marinobacter sp. Strain from Honolulu Harbor, Hawai'i. Genome Announc 2016; 4:e01354-16. [PMID: 27932650 DOI: 10.1128/genomeA.01354-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Marinobacter sp. strain X15-166BT was cultivated from sediment in Honolulu Harbor, Hawai‘i. The X15-166BT draft genome of 3,490,661 bp encodes 3,115 protein-coding open reading frames. We anticipate that the genome will provide insights into the strain’s lifestyle and the evolution of Marinobacter.
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19
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Wan X, Lee AJ, Hou S, Ushijima B, Nguyen YP, Thawley JA, Donachie SP. Draft Genome Sequence of Piscirickettsia litoralis, Isolated from Seawater. Genome Announc 2016; 4:e01252-16. [PMID: 27811116 DOI: 10.1128/genomeA.01252-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
One species of Piscirickettsia, a pathogen of salmonid fish, has been described. The genome sequence of a putative second and free-living species may provide insights into the evolution of pathogenicity in the genus.
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20
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Wan X, Miller JM, Rowley SJ, Hou S, Donachie SP. Draft Genome Sequence of a Novel Luteimonas sp. Strain from Coral Mucus, Hawai'i. Genome Announc 2016; 4:e01228-16. [PMID: 27811107 DOI: 10.1128/genomeA.01228-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Luteimonas sp. strain JM171 was cultivated from mucus collected around the coral Porites lobata The JM171 draft genome of 2,992,353 bp contains 2,672 protein-coding open reading frames, 45 tRNA coding regions, and encodes a putative globin-coupled diguanylate cyclase, JmGReg.
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21
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Wan X, Dasilveira L, Hou S, Saito JA, Donachie SP. Draft Genome Sequence of Terasakiispira papahanaumokuakeensis PH27AT, a Spiral Bacterium from the Northwestern Hawaiian Islands. Genome Announc 2016; 4:e01166-16. [PMID: 27795280 DOI: 10.1128/genomeA.01166-16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The genus Terasakiispira hosts only Terasakiispira papahanaumokuakeensis PH27AT, cultivated from an anchialine pond on Pearl and Hermes Atoll, Northwestern Hawaiian Islands. The strain’s genome sequence may provide insights into the evolution of free-living Oceanospirillaceae.
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22
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Wan X, Hou S, Saito JA, Kaneshiro KY, Donachie SP. Genome Sequence of Flavobacterium akiainvivens IK-1T, Isolated from Decaying Wikstroemia oahuensis, an Endemic Hawaiian Shrub. Genome Announc 2015; 3:e01222-15. [PMID: 26494668 DOI: 10.1128/genomeA.01222-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Flavobacterium spp. have been cultivated from diverse aquatic and terrestrial habitats. F. akiainvivens IK-1T was cultivated from decaying wood of Wikstroemia oahuensis, an endemic Hawaiian shrub. The strain’s genome sequence may provide insights into niche adaptation and evolution of the genus in a mid-ocean archipelago.
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23
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Teh BS, Lau NS, Ng FL, Abdul Rahman AY, Wan X, Saito JA, Hou S, Teh AH, Najimudin N, Alam M. Complete genome sequence of the thermophilic Thermus sp. CCB_US3_UF1 from a hot spring in Malaysia. Stand Genomic Sci 2015; 10:76. [PMID: 26457128 PMCID: PMC4599208 DOI: 10.1186/s40793-015-0053-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 07/28/2015] [Indexed: 02/08/2023] Open
Abstract
Thermus sp. strain CCB_US3_UF1 is a thermophilic bacterium of the genus Thermus, a member of the family Thermaceae. Members of the genus Thermus have been widely used as a biological model for structural biology studies and to understand the mechanism of microbial adaptation under thermal environments. Here, we present the complete genome sequence of Thermus sp. CCB_US3_UF1 isolated from a hot spring in Malaysia, which is the fifth member of the genus Thermus with a completely sequenced and publicly available genome (Genbank date of release: December 2, 2011). Thermus sp. CCB_US3_UF1 has the third largest genome within the genus. The complete genome comprises of a chromosome of 2.26 Mb and a plasmid of 19.7 kb. The genome contains 2279 protein-coding and 54 RNA genes. In addition, its genome revealed potential pathways for the synthesis of secondary metabolites (isoprenoid) and pigments (carotenoid).
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Affiliation(s)
- Beng Soon Teh
- Centre for Chemical Biology, Universiti Sains Malaysia, Penang, Malaysia ; Present address: Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Nyok-Sean Lau
- Centre for Chemical Biology, Universiti Sains Malaysia, Penang, Malaysia
| | - Fui Ling Ng
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | | | - Xuehua Wan
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii USA
| | - Jennifer A Saito
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii USA
| | - Shaobin Hou
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii USA
| | - Aik-Hong Teh
- Centre for Chemical Biology, Universiti Sains Malaysia, Penang, Malaysia
| | - Nazalan Najimudin
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Maqsudul Alam
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii USA ; Department of Microbiology, University of Hawaii, Honolulu, Hawaii USA
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Wan X, Hou S, Phan N, Malone Moss JS, Donachie SP, Alam M. Draft Genome Sequence of Pantoea anthophila Strain 11-2 from Hypersaline Lake Laysan, Hawaii. Genome Announc 2015; 3:e00321-15. [PMID: 25977417 DOI: 10.1128/genomeA.00321-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Most Pantoea spp. have been isolated from plant sources or clinical samples. However, we cultivated Pantoea anthophila 11-2 from hypersaline water from the lake on Laysan, Northwestern Hawaiian Islands. Draft genome sequencing of 11-2 provides a molecular basis for studies in evolution and pathogenicity in Pantoea spp.
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Wan X, Qian L, Hou S, Drees KP, Foster JT, Douglas JT. Complete Genome Sequences of Beijing and Manila Family Strains of Mycobacterium tuberculosis. Genome Announc 2014; 2:e01135-14. [PMID: 25395630 DOI: 10.1128/genomeA.01135-14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The majority of isolates from tuberculosis patients in Hawaii arrive through the immigration of infected individuals from the western Pacific. We report here on the annotated complete genomes of two strains of Mycobacterium tuberculosis from the two main lineages/families in Hawaii, Beijing and Manila.
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Saw JHW, Schatz M, Brown MV, Kunkel DD, Foster JS, Shick H, Christensen S, Hou S, Wan X, Donachie SP. Cultivation and complete genome sequencing of Gloeobacter kilaueensis sp. nov., from a lava cave in Kīlauea Caldera, Hawai'i. PLoS One 2013; 8:e76376. [PMID: 24194836 PMCID: PMC3806779 DOI: 10.1371/journal.pone.0076376] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 08/24/2013] [Indexed: 02/05/2023] Open
Abstract
The ancestor of Gloeobacter violaceus PCC 7421T is believed to have diverged from that of all known cyanobacteria before the evolution of thylakoid membranes and plant plastids. The long and largely independent evolutionary history of G. violaceus presents an organism retaining ancestral features of early oxygenic photoautotrophs, and in whom cyanobacteria evolution can be investigated. No other Gloeobacter species has been described since the genus was established in 1974 (Rippka et al., Arch Microbiol 100:435). Gloeobacter affiliated ribosomal gene sequences have been reported in environmental DNA libraries, but only the type strain's genome has been sequenced. However, we report here the cultivation of a new Gloeobacter species, G. kilaueensis JS1T, from an epilithic biofilm in a lava cave in Kīlauea Caldera, Hawai'i. The strain's genome was sequenced from an enriched culture resembling a low-complexity metagenomic sample, using 9 kb paired-end 454 pyrosequences and 400 bp paired-end Illumina reads. The JS1T and G. violaceus PCC 7421T genomes have little gene synteny despite sharing 2842 orthologous genes; comparing the genomes shows they do not belong to the same species. Our results support establishing a new species to accommodate JS1T, for which we propose the name Gloeobacter kilaueensis sp. nov. Strain JS1T has been deposited in the American Type Culture Collection (BAA-2537), the Scottish Marine Institute's Culture Collection of Algae and Protozoa (CCAP 1431/1), and the Belgian Coordinated Collections of Microorganisms (ULC0316). The G. kilaueensis holotype has been deposited in the Algal Collection of the US National Herbarium (US# 217948). The JS1T genome sequence has been deposited in GenBank under accession number CP003587. The G+C content of the genome is 60.54 mol%. The complete genome sequence of G. kilaueensis JS1T may further understanding of cyanobacteria evolution, and the shift from anoxygenic to oxygenic photosynthesis.
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Affiliation(s)
- Jimmy H. W. Saw
- Department of Microbiology, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States of America
| | - Michael Schatz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Mark V. Brown
- NASA Astrobiology Institute, University of Hawai'i, Honolulu, Hawai'i, United States of America
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - Dennis D. Kunkel
- Dennis Kunkel Microscopy, Inc., Kailua, Hawai'i, United States of America
| | - Jamie S. Foster
- Department of Microbiology and Cell Science, University of Florida Space Life Science Laboratory, Kennedy Space Center, Kennedy, Florida, United States of America
| | | | - Stephanie Christensen
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, Hawai'I, United States of America
| | - Shaobin Hou
- Department of Microbiology, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States of America
- Advanced Studies of Genomics, Proteomics and Bioinformatics, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States of America
| | - Xuehua Wan
- Department of Microbiology, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States of America
- Advanced Studies of Genomics, Proteomics and Bioinformatics, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States of America
| | - Stuart P. Donachie
- Department of Microbiology, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States of America
- * E-mail:
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Ong SY, Pratap CB, Wan X, Hou S, Rahman AYA, Saito JA, Nath G, Alam M. The Genomic Blueprint of Salmonella enterica subspecies enterica serovar Typhi P-stx-12. Stand Genomic Sci 2013; 7:483-96. [PMID: 24019994 PMCID: PMC3764930 DOI: 10.4056/sigs.3286690] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Salmonella enterica subspecies enterica serovar Typhi is a rod-shaped, Gram-negative, facultatively anaerobic bacterium. It belongs to the family Enterobacteriaceae in the class Gammaproteobacteria, and has the capability of residing in the human gallbladder by forming a biofilm and hence causing the person to become a typhoid carrier. Here we present the complete genome of Salmonella enterica subspecies enterica serotype Typhi strain P-stx-12, which was isolated from a chronic carrier in Varanasi, India. The complete genome comprises a 4,768,352 bp chromosome with a total of 98 RNA genes, 4,691 protein-coding genes and a 181,431 bp plasmid. Genome analysis revealed that the organism is closely related to Salmonella enterica serovar Typhi strain Ty2 and Salmonella enterica serovar Typhi strain CT18, although their genome structure is slightly different.
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Affiliation(s)
- Su Yean Ong
- Centre for Chemical Biology, Universiti Sains Malaysia, Penang, Malaysia
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Islam MS, Haque MS, Islam MM, Emdad EM, Halim A, Hossen QMM, Hossain MZ, Ahmed B, Rahim S, Rahman MS, Alam MM, Hou S, Wan X, Saito JA, Alam M. Tools to kill: genome of one of the most destructive plant pathogenic fungi Macrophomina phaseolina. BMC Genomics 2012; 13:493. [PMID: 22992219 PMCID: PMC3477038 DOI: 10.1186/1471-2164-13-493] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 09/13/2012] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Macrophomina phaseolina is one of the most destructive necrotrophic fungal pathogens that infect more than 500 plant species throughout the world. It can grow rapidly in infected plants and subsequently produces a large amount of sclerotia that plugs the vessels, resulting in wilting of the plant. RESULTS We sequenced and assembled ~49 Mb into 15 super-scaffolds covering 92.83% of the M. phaseolina genome. We predict 14,249 open reading frames (ORFs) of which 9,934 are validated by the transcriptome. This phytopathogen has an abundance of secreted oxidases, peroxidases, and hydrolytic enzymes for degrading cell wall polysaccharides and lignocelluloses to penetrate into the host tissue. To overcome the host plant defense response, M. phaseolina encodes a significant number of P450s, MFS type membrane transporters, glycosidases, transposases, and secondary metabolites in comparison to all sequenced ascomycete species. A strikingly distinct set of carbohydrate esterases (CE) are present in M. phaseolina, with the CE9 and CE10 families remarkably higher than any other fungi. The phenotypic microarray data indicates that M. phaseolina can adapt to a wide range of osmotic and pH environments. As a broad host range pathogen, M. phaseolina possesses a large number of pathogen-host interaction genes including those for adhesion, signal transduction, cell wall breakdown, purine biosynthesis, and potent mycotoxin patulin. CONCLUSIONS The M. phaseolina genome provides a framework of the infection process at the cytological and molecular level which uses a diverse arsenal of enzymatic and toxin tools to destroy the host plants. Further understanding of the M. phaseolina genome-based plant-pathogen interactions will be instrumental in designing rational strategies for disease control, essential to ensuring global agricultural crop production and security.
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Affiliation(s)
- Md Shahidul Islam
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka 1207, Bangladesh
| | - Md Samiul Haque
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka 1207, Bangladesh
| | - Mohammad Moinul Islam
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka 1207, Bangladesh
| | - Emdadul Mannan Emdad
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka 1207, Bangladesh
| | - Abdul Halim
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka 1207, Bangladesh
| | - Quazi Md Mosaddeque Hossen
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka 1207, Bangladesh
| | - Md Zakir Hossain
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka 1207, Bangladesh
| | - Borhan Ahmed
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka 1207, Bangladesh
| | - Sifatur Rahim
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka 1207, Bangladesh
| | - Md Sharifur Rahman
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka 1207, Bangladesh
| | - Md Monjurul Alam
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka 1207, Bangladesh
| | - Shaobin Hou
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, 2565 McCarthy Mall, Keller 319, Honolulu, Hawaii 96822, USA
| | - Xuehua Wan
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, 2565 McCarthy Mall, Keller 319, Honolulu, Hawaii 96822, USA
| | - Jennifer A Saito
- Centre for Chemical Biology, Universiti Sains Malaysia, Penang, 11800, Malaysia
| | - Maqsudul Alam
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka 1207, Bangladesh
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, 2565 McCarthy Mall, Keller 319, Honolulu, Hawaii 96822, USA
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Ong SY, Pratap CB, Wan X, Hou S, Abdul Rahman AY, Saito JA, Nath G, Alam M. Complete genome sequence of Salmonella enterica subsp. enterica serovar Typhi P-stx-12. J Bacteriol 2012; 194:2115-6. [PMID: 22461552 DOI: 10.1128/JB.00121-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We report here the complete genome sequence of Salmonella enterica subsp. enterica serovar Typhi P-stx-12, a clinical isolate obtained from a typhoid carrier in India.
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Tuckerman JR, Gonzalez G, Sousa EHS, Wan X, Saito JA, Alam M, Gilles-Gonzalez MA. An oxygen-sensing diguanylate cyclase and phosphodiesterase couple for c-di-GMP control. Biochemistry 2009; 48:9764-74. [PMID: 19764732 DOI: 10.1021/bi901409g] [Citation(s) in RCA: 173] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A commonly observed coupling of sensory domains to GGDEF-class diguanylate cyclases and EAL-class phosphodiesterases has long suggested that c-di-GMP synthesizing and degrading enzymes sense environmental signals. Nevertheless, relatively few signal ligands have been identified for these sensors, and even fewer instances of in vitro switching by ligand have been demonstrated. Here we describe an Escherichia coli two-gene operon, dosCP, for control of c-di-GMP by oxygen. In this operon, the gene encoding the oxygen-sensing c-di-GMP phosphodiesterase Ec Dos (here renamed Ec DosP) follows and is translationally coupled to a gene encoding a diguanylate cyclase, here designated DosC. We present the first characterizations of DosC and a detailed study of the ligand-dose response of DosP. Our results show that DosC is a globin-coupled sensor with an apolar but accessible heme pocket that binds oxygen with a K(d) of 20 microM. The response of DosP activation to increasing oxygen concentration is a complex function of its ligand saturation such that over 80% of the activation occurs in solutions that exceed 30% of air saturation (oxygen >75 microM). Finally, we find that DosP and DosC associate into a functional complex. We conclude that the dosCP operon encodes two oxygen sensors that cooperate in the controlled production and removal of c-di-GMP.
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Affiliation(s)
- Jason R Tuckerman
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9038, USA
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Wan X, Tuckerman JR, Saito JA, Freitas TAK, Newhouse JS, Denery JR, Galperin MY, Gonzalez G, Gilles-Gonzalez MA, Alam M. Globins synthesize the second messenger bis-(3'-5')-cyclic diguanosine monophosphate in bacteria. J Mol Biol 2009; 388:262-70. [PMID: 19285985 DOI: 10.1016/j.jmb.2009.03.015] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Revised: 02/28/2009] [Accepted: 03/09/2009] [Indexed: 02/08/2023]
Abstract
Globin-coupled sensors are heme-binding signal transducers in Bacteria and Archaea in which an N-terminal globin controls the activity of a variable C-terminal domain. Here, we report that BpeGReg, a globin-coupled diguanylate cyclase from the whooping cough pathogen Bordetella pertussis, synthesizes the second messenger bis-(3'-5')-cyclic diguanosine monophosphate (c-di-GMP) upon oxygen binding. Expression of BpeGReg in Salmonella typhimurium enhances biofilm formation, while knockout of the BpeGReg gene of B. pertussis results in decreased biofilm formation. These results represent the first identification a signal ligand for any diguanylate cyclase and provide definitive experimental evidence that a globin-coupled sensor regulates c-di-GMP synthesis and biofilm formation. We propose that the synthesis of c-di-GMP by globin sensors is a widespread phenomenon in bacteria.
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Affiliation(s)
- Xuehua Wan
- Department of Microbiology, University of Hawaii, 2538 McCarthy Mall, Snyder Hall 207, Honolulu, HI 96822, USA
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Pesce A, Thijs L, Nardini M, Desmet F, Sisinni L, Gourlay L, Bolli A, Coletta M, Van Doorslaer S, Wan X, Alam M, Ascenzi P, Moens L, Bolognesi M, Dewilde S. HisE11 and HisF8 provide bis-histidyl heme hexa-coordination in the globin domain of Geobacter sulfurreducens globin-coupled sensor. J Mol Biol 2008; 386:246-60. [PMID: 19109973 DOI: 10.1016/j.jmb.2008.12.023] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Revised: 12/05/2008] [Accepted: 12/09/2008] [Indexed: 02/08/2023]
Abstract
Among heme-based sensors, recent phylogenomic and sequence analyses have identified 34 globin coupled sensors (GCS), to which an aerotactic or gene-regulating function has been tentatively ascribed. Here, the structural and biochemical characterization of the globin domain of the GCS from Geobacter sulfurreducens (GsGCS(162)) is reported. A combination of X-ray crystallography (crystal structure at 1.5 A resolution), UV-vis and resonance Raman spectroscopy reveals the ferric GsGCS(162) as an example of bis-histidyl hexa-coordinated GCS. In contrast to the known hexa-coordinated globins, the distal heme-coordination in ferric GsGCS(162) is provided by a His residue unexpectedly located at the E11 topological site. Furthermore, UV-vis and resonance Raman spectroscopy indicated that ferrous deoxygenated GsGCS(162) is a penta-/hexa-coordinated mixture, and the heme hexa-to-penta-coordination transition does not represent a rate-limiting step for carbonylation kinetics. Lastly, electron paramagnetic resonance indicates that ferrous nitrosylated GsGCS(162) is a penta-coordinated species, where the proximal HisF8-Fe bond is severed.
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Affiliation(s)
- Alessandra Pesce
- Department of Physics, CNISM and Center for Excellence in Biomedical Research, University of Genova, Via Dodecaneso, 33, I-16146 Genova, Italy
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Saito JA, Wan X, Lee KS, Hou S, Alam M. Globin-coupled sensors and protoglobins share a common signaling mechanism. FEBS Lett 2008; 582:1840-6. [PMID: 18486614 DOI: 10.1016/j.febslet.2008.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2008] [Revised: 04/28/2008] [Accepted: 05/06/2008] [Indexed: 02/08/2023]
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Thijs L, Vinck E, Bolli A, Trandafir F, Wan X, Hoogewijs D, Coletta M, Fago A, Weber RE, Van Doorslaer S, Ascenzi P, Alam M, Moens L, Dewilde S. Characterization of a globin-coupled oxygen sensor with a gene-regulating function. J Biol Chem 2007; 282:37325-40. [PMID: 17925395 DOI: 10.1074/jbc.m705541200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Globin-coupled sensors (GCSs) are multiple-domain transducers, consisting of a regulatory globin-like heme-binding domain and a linked transducer domain(s). GCSs have been described in both Archaea and bacteria. They are generally assumed to bind O(2) (and perhaps other gaseous ligands) and to transmit a conformational change signal through the transducer domain in response to fluctuating O(2) levels. In this study, the heme-binding domain, AvGReg178, and the full protein, AvGReg of the Azotobacter vinelandii GCS, were cloned, expressed, and purified. After purification, the heme iron of AvGReg178 was found to bind O(2). This form was stable over many hours. In contrast, the predominant presence of a bis-histidine coordinate heme in ferric AvGReg was revealed. Differences in the heme pocket structure were also observed for the deoxygenated ferrous state of these proteins. The spectra showed that the deoxygenated ferrous derivatives of AvGReg178 and AvGReg are characterized by a penta-coordinate and hexa-coordinate heme iron, respectively. O(2) binding isotherms indicate that AvGReg178 and AvGReg show a high affinity for O(2) with P(50) values at 20 degrees C of 0.04 and 0.15 torr, respectively. Kinetics of CO binding indicate that AvGReg178 carbonylation conforms to a monophasic process, comparable with that of myoglobin, whereas AvGReg carbonylation conforms to a three-phasic reaction, as observed for several proteins with bis-histidine heme iron coordination. Besides sensing ligands, in vitro data suggest that AvGReg(178) may have a role in O(2)-mediated NO-detoxification, yielding metAvGReg(178) and nitrate.
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Affiliation(s)
- Liesbet Thijs
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium
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