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Zhou Q, Mai K, Yang D, Liu J, Yan Z, Luo C, Tan Y, Cao S, Zhou Q, Chen L, Chen F. Comparative genomic analysis of Mycoplasma anatis strains. Genes Genomics 2021; 43:1327-1337. [PMID: 34181213 PMCID: PMC8237044 DOI: 10.1007/s13258-021-01129-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 06/18/2021] [Indexed: 12/01/2022]
Abstract
Background The Gram-negative intracellular bacterium Mycoplasma anatis is a pathogen of respiratory infectious diseases in ducks and has caused significant economic losses in the poultry industry. Objective This study, as the first report of the structure and function of the pan-genome of Mycoplasma anatis, may provide a valuable genetic basis for many aspects of future research on the pathogens of waterfowl. Methods We sequenced the whole genomes of 15 Mycoplasma anatis isolated from ducks in China. Draft genome sequencing was carried out and whole-genome sequencing was performed by the sequencers of the PacBio Sequel and an IonTorrent Personal Genome Machine (PGM). Then the common genic elements of protein-coding genes, tRNAs, and rRNAs of Mycoplasma anatis genomes were predicted by using the pipeline Prokka v1.13.7. To investigate homologous protein clusters across Mycoplasma anatis genomes, we adopted Roary v3.13.0 to cluster orthologous genes (OGs) based on the following criteria. Results We obtained one complete genome and 14 genome sketches. Microbial mobile genetic element analysis revealed the distribution of insertion sequences (IS30, IS3, and IS1634), prophage regions, and CRISPR arrays in the genome of Mycoplasma anatis. Comparative genomic analysis decoded the genetic components and functional classification of the pan-genome of Mycoplasma anatis that comprised 646 core genes, 231 dispensable genes and among them 110 was strain-specific. Virulence-related gene profiles of Mycoplasma anatis were systematically identified, and the products of these genes included bacterial ABC transporter systems, iron transport proteins, toxins, and secretion systems. Conclusion A complete virulence-related gene profile of Mycoplasma anatis has been identified, most of the genes are highly conserved in all strains. Sequencing results are relevant to the molecular mechanisms of drug resistance, adaptive evolution of pathogens, population structure, and vaccine development. Supplementary Information The online version contains supplementary material available at 10.1007/s13258-021-01129-5.
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Affiliation(s)
- Qi Zhou
- Guangdong Enterprise Key Laboratory for Animal Health and Environmental Control, Wen's Foodstuff Group Co. Ltd, Yunfu, 527400, China
| | - Kaijie Mai
- Guangdong Enterprise Key Laboratory for Animal Health and Environmental Control, Wen's Foodstuff Group Co. Ltd, Yunfu, 527400, China.,College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Dehong Yang
- Guangdong Enterprise Key Laboratory for Animal Health and Environmental Control, Wen's Foodstuff Group Co. Ltd, Yunfu, 527400, China
| | - Junfa Liu
- Guangdong Enterprise Key Laboratory for Animal Health and Environmental Control, Wen's Foodstuff Group Co. Ltd, Yunfu, 527400, China
| | - Zhuanqiang Yan
- Guangdong Enterprise Key Laboratory for Animal Health and Environmental Control, Wen's Foodstuff Group Co. Ltd, Yunfu, 527400, China
| | - Cuifen Luo
- Guangdong Enterprise Key Laboratory for Animal Health and Environmental Control, Wen's Foodstuff Group Co. Ltd, Yunfu, 527400, China
| | - Yangtong Tan
- Guangdong Enterprise Key Laboratory for Animal Health and Environmental Control, Wen's Foodstuff Group Co. Ltd, Yunfu, 527400, China
| | - Sheng Cao
- Guangdong Enterprise Key Laboratory for Animal Health and Environmental Control, Wen's Foodstuff Group Co. Ltd, Yunfu, 527400, China
| | - Qingfeng Zhou
- Guangdong Enterprise Key Laboratory for Animal Health and Environmental Control, Wen's Foodstuff Group Co. Ltd, Yunfu, 527400, China.
| | - Li Chen
- Guangdong Enterprise Key Laboratory for Animal Health and Environmental Control, Wen's Foodstuff Group Co. Ltd, Yunfu, 527400, China
| | - Feng Chen
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
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Lou J, Liu M, Gu J, Liu Q, Zhao L, Ma Y, Wei D. Metagenomic sequencing reveals microbial gene catalogue of phosphinothricin-utilized soils in South China. Gene 2019; 711:143942. [DOI: 10.1016/j.gene.2019.143942] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 06/04/2019] [Accepted: 06/19/2019] [Indexed: 11/17/2022]
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Abstract
It is estimated that approximately one billion people are at risk of infection with obligate intracellular bacteria, but little is known about the underlying mechanisms that govern their life cycles. The difficulty in studying Chlamydia spp., Coxiella spp., Rickettsia spp., Anaplasma spp., Ehrlichia spp. and Orientia spp. is, in part, due to their genetic intractability. Recently, genetic tools have been developed; however, optimizing the genomic manipulation of obligate intracellular bacteria remains challenging. In this Review, we describe the progress in, as well as the constraints that hinder, the systematic development of a genetic toolbox for obligate intracellular bacteria. We highlight how the use of genetically manipulated pathogens has facilitated a better understanding of microbial pathogenesis and immunity, and how the engineering of obligate intracellular bacteria could enable the discovery of novel signalling circuits in host-pathogen interactions.
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Poehlein A, Freese H, Daniel R, Simeonova DD. Genome sequence of Shinella sp. strain DD12, isolated from homogenized guts of starved Daphnia magna. Stand Genomic Sci 2016; 11:14. [PMID: 26865909 PMCID: PMC4748535 DOI: 10.1186/s40793-015-0129-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 12/30/2015] [Indexed: 11/10/2022] Open
Abstract
Shinella sp. strain DD12, a novel phosphite assimilating bacterium, has been isolated from homogenized guts of 4 days starved zooplankton Daphnia magna. Here we report the draft genome of this bacterium, which comprises 7,677,812 bp and 7505 predicted protein-coding genes.
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Affiliation(s)
- Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University Göttingen, D-37077 Göttingen, Germany
| | - Heike Freese
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, 38124 Braunschweig, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University Göttingen, D-37077 Göttingen, Germany
| | - Diliana D Simeonova
- Laboratory of Microbial Ecology, University of Konstanz, D-78457 Constance, Germany ; Current Address: Laboratory of Microbial Biochemistry, Department of General Microbiology, Institute of Microbiology, Bulgarian Academy of Sciences, 26 Georgi Bonchev str., 1113 Sofia, Bulgaria
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Lewis JP. Metal uptake in host-pathogen interactions: role of iron in Porphyromonas gingivalis interactions with host organisms. Periodontol 2000 2010; 52:94-116. [PMID: 20017798 DOI: 10.1111/j.1600-0757.2009.00329.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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6
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Desrosiers DC, Sun YC, Zaidi AA, Eggers CH, Cox DL, Radolf JD. The general transition metal (Tro) and Zn2+(Znu) transporters inTreponema pallidum: analysis of metal specificities and expression profiles. Mol Microbiol 2007; 65:137-52. [PMID: 17581125 DOI: 10.1111/j.1365-2958.2007.05771.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Acquisition of transition metals is central to the struggle between a bacterial pathogen and its mammalian host. Previous studies demonstrated that Treponema pallidum encodes a cluster-9 (C9) ABC transporter (troABCD) whose solute-binding protein component (TroA) ligands Zn(2+) and Mn(2+) with essentially equal affinities. Bioinformatic analysis revealed that T. pallidum encodes an additional C9 transporter (tp0034-36) orthologous to Zn(2+)-uptake (Znu) systems in other bacteria; the binding protein component, ZnuA, contains a His-rich tract characteristic of C9 Zn(2+)-binding proteins. Metal analysis and metal-reconstitution studies demonstrated that ZnuA is a Zn(2+)-binding protein; parallel studies confirmed that TroA binds Zn(2+), Mn(2+) and Fe. Circular dichroism showed that ZnuA, but not TroA, undergoes conformational changes in the presence of Zn(2+). Using isothermal titration calorimetry (ITC), we demonstrated that TroA binds Zn(2+) and Mn(2+) with affinities approximately 100-fold greater than those previously reported. ITC analysis revealed that ZnuA contains multiple Zn(2+)-binding sites, two of which are high-affinity and presumed to be located within the binding pocket and His-rich loop. Quantitative reverse transcription polymerase chain reaction of tro and znu transcripts combined with immunoblot analysis of TroA and ZnuA confirmed that both transporters are simultaneously expressed in T. pallidum and that TroA is expressed at much greater levels than ZnuA. Collectively, our findings indicate that T. pallidum procures transition metals via the concerted utilization of its general metal (Tro) and Zn(2+) (Znu) transporters. Sequestration of periplasmic Zn(2+) by ZnuA may free up TroA binding capacity for the importation of Fe and Mn(2+).
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Affiliation(s)
- Daniel C Desrosiers
- Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, CT 06030-3715, USA
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Lewis JP, Plata K, Yu F, Rosato A, Anaya C. Transcriptional organization, regulation and role of the Porphyromonas gingivalis W83 hmu haemin-uptake locus. MICROBIOLOGY-SGM 2007; 152:3367-3382. [PMID: 17074906 DOI: 10.1099/mic.0.29011-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Porphyromonas gingivalis, an oral bacterium associated with periodontal disease, requires haemin for growth. Although several multigenic clusters encoding haemin-uptake systems are present on the genome of P. gingivalis, little is known regarding their transcriptional organization and expression. This study identified a 23 kDa iron-regulated haemin-binding protein encoded by a larger than previously reported variant of hmuY. It was shown that the hmu locus is larger than previously reported and is composed of six genes, hmuYRSTUV, encoding a novel hybrid haemin-uptake system. The locus has an operonic organization and the transcriptional start site is located 292 bp upstream of hmuY. The data indicate that the regulation of the operon is iron-dependent. Interestingly, differential regulation within the operon was demonstrated, resulting in excess of the hmuYR message encoding the outer-membrane proteins when compared to the full-length transcript. In addition, the hmuY transcript is more prevalent than the hmuR transcript. Secondary structure analysis of the hmuYRSTUV mRNA predicted the formation of several potential stem-loops in the 5' ends of hmuR- and hmuS-specific mRNAs, consistent with the differential regulation observed. Finally, it was demonstrated that haemin binding and uptake are elevated in iron-depleted conditions and are reduced 45 % and 70 %, respectively, in an hmu-deficient strain when compared to the parental strain, indicating that the hmu locus plays a major role in haemin acquisition in P. gingivalis. Since homologues of the hmu locus were also found in Bacteroides fragilis, Bacteroides thetaiotaomicron and Prevotella intermedia, these findings may have implications for a better understanding of haemin acquisition in those organisms as well.
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Affiliation(s)
- Janina P Lewis
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
- The Philips Institute, Virginia Commonwealth University, Richmond, VA, USA
| | - Konrad Plata
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
- The Philips Institute, Virginia Commonwealth University, Richmond, VA, USA
| | - Fan Yu
- The Philips Institute, Virginia Commonwealth University, Richmond, VA, USA
| | - Adriana Rosato
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - Cecilia Anaya
- University of San Luis, San Luis, Argentina
- The Philips Institute, Virginia Commonwealth University, Richmond, VA, USA
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Yoon KH, Cho JY. Transcriptional analysis of the gum gene cluster from Xanthomonas oryzae pathovar oryzae. Biotechnol Lett 2006; 29:95-103. [PMID: 17091379 DOI: 10.1007/s10529-006-9217-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2006] [Accepted: 09/19/2006] [Indexed: 10/23/2022]
Abstract
Genome sequence analysis of Xanthomonas oryzae pv. oryzae KACC10331 provides insight into the X. oryzae gum gene cluster that is composed of 14 open-reading frames (ORFs), designated gumB, -C, -D, -E, -F, -G, -H, -I, -J, -K, -L, -M, XOO3167, and -N. We analyzed the transcriptional linkage of the X. oryzae gum gene cluster by using RT-PCR. Analyses of the gum gene cluster by RT-PCR with the wild-type and mutant strains, which carried a deletion of the promoter-like region upstream of gumB or an insertion of the rrnB transcriptional terminator into the gumF gene, revealed that the ORFs of this gene cluster were transcribed as polycistronic mRNA, from gumB to gumN, and the secondary promoter was located upstream of gumG. Taken together, these results suggest that the genes of this cluster constitute an operon expressed from overlapping transcripts.
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Affiliation(s)
- Ki-Hoon Yoon
- Division of Animal Science and Biotechnology, Sangji University, Wonju-si, Gangwon-do, Korea
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Anderson DS, Adhikari P, Nowalk AJ, Chen CY, Mietzner TA. The hFbpABC transporter from Haemophilus influenzae functions as a binding-protein-dependent ABC transporter with high specificity and affinity for ferric iron. J Bacteriol 2004; 186:6220-9. [PMID: 15342592 PMCID: PMC515168 DOI: 10.1128/jb.186.18.6220-6229.2004] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2004] [Accepted: 06/09/2004] [Indexed: 11/20/2022] Open
Abstract
Pathogenic Haemophilus influenzae, Neisseria spp. (Neisseria gonorrhoeae and N. meningitidis), Serratia marcescens, and other gram-negative bacteria utilize a periplasm-to-cytosol FbpABC iron transporter. In this study, we investigated the H. influenzae FbpABC transporter in a siderophore-deficient Escherichia coli background to assess biochemical aspects of FbpABC transporter function. Using a radiolabeled Fe3+ transport assay, we established an apparent Km=0.9 microM and Vmax=1.8 pmol/10(7)cells/min for FbpABC-mediated transport. Complementation experiments showed that hFbpABC is dependent on the FbpA binding protein for transport. The ATPase inhibitor sodium orthovanadate demonstrated dose-dependent inhibition of FbpABC transport, while the protonmotive-force-inhibitor carbonyl cyanide m-chlorophenyl hydrazone had no effect. Metal competition experiments demonstrated that the transporter has high specificity for Fe3+ and selectivity for trivalent metals, including Ga3+ and Al3+, over divalent metals. Metal sensitivity experiments showed that several divalent metals, including copper, nickel, and zinc, exhibited general toxicity towards E. coli. Significantly, gallium-induced toxicity was specific only to E. coli expressing FbpABC. A single-amino-acid mutation in the gene encoding the periplasmic binding protein, FbpA(Y196I), resulted in a greatly diminished iron binding affinity Kd=5.2 x 10(-4) M(-1), approximately 14 orders of magnitude weaker than that of the wild-type protein. Surprisingly, the mutant transporter [FbpA(Y196I)BC] exhibited substantial transport activity, approximately 35% of wild-type transport, with Km=1.2 microM and Vmax=0.5 pmol/10(7)cells/min. We conclude that the FbpABC complexes possess basic characteristics representative of the family of bacterial binding protein-dependent ABC transporters. However, the specificity and high-affinity binding characteristics suggest that the FbpABC transporters function as specialized transporters satisfying the strict chemical requirements of ferric iron (Fe3+) binding and membrane transport.
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Affiliation(s)
- Damon S Anderson
- Department of Molecular Genetics and Biochemistry, University of Pittsburgh School of Medicine, Room E1240 Biomedical Science Tower, Lothrop St., Pittsburgh, PA 15261, USA
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Lau GHY, MacGillivray RTA, Murphy MEP. Characterization of a nucleotide-binding domain associated with neisserial iron transport. J Bacteriol 2004; 186:3266-9. [PMID: 15126492 PMCID: PMC400613 DOI: 10.1128/jb.186.10.3266-3269.2004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The fbpABC operon in Neisseria gonorrhoeae encodes an ATP-binding cassette transporter required for iron uptake from the host ferric binding proteins. The gene for the nucleotide-binding domain (fbpC) expressed in Escherichia coli has intrinsic ATPase activity (0.5 mmol/min/mg) uncoupled from the iron transport process. The FbpC E164D mutant is found to have a 10-fold reduction in specific activity. FbpC is covalently modified by 8-azido-[gamma32P]ATP, indicating that FbpC is a functional ATPase that likely combines with FbpB to form a ferric iron transporter.
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Affiliation(s)
- Gloria H Y Lau
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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Perkins-Balding D, Ratliff-Griffin M, Stojiljkovic I. Iron transport systems in Neisseria meningitidis. Microbiol Mol Biol Rev 2004; 68:154-71. [PMID: 15007100 PMCID: PMC362107 DOI: 10.1128/mmbr.68.1.154-171.2004] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acquisition of iron and iron complexes has long been recognized as a major determinant in the pathogenesis of Neisseria meningitidis. In this review, high-affinity iron uptake systems, which allow meningococci to utilize the human host proteins transferrin, lactoferrin, hemoglobin, and haptoglobin-hemoglobin as sources of essential iron, are described. Classic features of bacterial iron transport systems, such as regulation by the iron-responsive repressor Fur and TonB-dependent transport activity, are discussed, as well as more specific features of meningococcal iron transport. Our current understanding of how N. meningitidis acquires iron from the human host and the vaccine potentials of various components of these iron transport systems are also reviewed.
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Affiliation(s)
- Donna Perkins-Balding
- Rollins Research Center, Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA.
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Shepard BD, Gilmore MS. Differential expression of virulence-related genes in Enterococcus faecalis in response to biological cues in serum and urine. Infect Immun 2002; 70:4344-52. [PMID: 12117944 PMCID: PMC128128 DOI: 10.1128/iai.70.8.4344-4352.2002] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enterococci rank among leading causes of nosocomial bacteremia and urinary tract infection and are also a leading cause of community acquired subacute endocarditis. Limited evidence suggests that biological cues in serum and urine may play an important role in modulating enterococcal virulence at sites of infection. To determine the extent to which biological cues affect enterococcal virulence-associated gene expression, we used quantitative real-time PCR to compare mRNA levels in Enterococcus faecalis cultures grown in serum or urine to that achieved in laboratory medium. Both environment- and growth phase-specific variations were observed, demonstrating the occurrence of as-yet-uncharacterized mechanisms for control of gene expression in E. faecalis that may play an important role in vivo.
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Affiliation(s)
- Brett D Shepard
- Department of Ophthalmology, Dean A. McGee Eye Institute, University of Oklahoma Health Sciences Center, Oklahoma City 73104, USA
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Ronpirin C, Jerse AE, Cornelissen CN. Gonococcal genes encoding transferrin-binding proteins A and B are arranged in a bicistronic operon but are subject to differential expression. Infect Immun 2001; 69:6336-47. [PMID: 11553578 PMCID: PMC98769 DOI: 10.1128/iai.69.10.6336-6347.2001] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Neisseria gonorrhoeae is capable of utilizing host iron-binding proteins, such as transferrin, lactoferrin, and hemoglobin, as the sole source of iron. The receptor involved in transferrin iron acquisition is composed of two distinct transferrin-binding proteins, TbpA and TbpB. The genes that encode these proteins are linked on the chromosome in the order tbpB-tbpA but are separated by an inverted repeat of unknown function. In this study, we sought to understand the transcriptional organization and regulation of the tbp genes, using a combination of lacZ transcriptional fusion analysis and reverse transcriptase PCR (RT-PCR). First, we demonstrated that tbpB and tbpA are cotranscribed and coregulated from the common upstream promoter that precedes tbpB. Using beta-galactosidase activity as a surrogate for tbp-specific transcription, we found that tbpB-specific transcripts were more prevalent than tbpA-specific transcripts after 2 h of growth under iron stress conditions. We confirmed the results obtained by fusion analysis by using RT-PCR applied to native RNA isolated from wild-type gonococci. Three different varieties of RT-PCR were employed: relative, competitive, and real time quantitative. The results of all analyses indicated that tbpB-specific transcripts were approximately twofold more prevalent than tbpA-specific transcripts at steady state. In iron-stressed cultures, the ratio of tbpB- to tbpA-specific message was approximately 2; however, in iron-replete cultures, this ratio dropped to 1. Using these techniques, we also quantitated the effects of iron, external pH, and presence of ligand on tbp mRNA levels.
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Affiliation(s)
- C Ronpirin
- Department of Microbiology and Immunology, Medical College of Virginia, Virginia Commonwealth University, Richmond, Virginia 23298-0678, USA
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