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Surdel MC, Coburn J. Leptospiral adhesins: from identification to future perspectives. Front Microbiol 2024; 15:1458655. [PMID: 39206373 PMCID: PMC11350617 DOI: 10.3389/fmicb.2024.1458655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Accepted: 08/01/2024] [Indexed: 09/04/2024] Open
Abstract
Leptospirosis is a significant zoonosis worldwide, with disease severity ranging from a mild non-specific illness to multi-organ dysfunction and hemorrhage. The disease is caused by pathogenic bacteria of the genus Leptospira, which are classified into pathogenic and saprophytic clades. Bacterial binding to host molecules and cells, coordinated by adhesin proteins, is an important step in pathogenesis. While many leptospiral adhesins have been identified, the vast majority have not been characterized in vivo. Herein, we present an overview of the current methodologies and successes in identifying adhesins in Leptospira, including known biological roles in vivo. We will also identify and discuss potential areas for future research.
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Affiliation(s)
- Matthew C. Surdel
- Division of Infectious Diseases, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Jenifer Coburn
- Division of Infectious Diseases, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
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An expanded reference map of the human gut microbiome reveals hundreds of previously unknown species. Nat Commun 2022; 13:3863. [PMID: 35790781 PMCID: PMC9256738 DOI: 10.1038/s41467-022-31502-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/16/2022] [Indexed: 11/22/2022] Open
Abstract
The gut is the richest ecosystem of microbes in the human body and has great influence on our health. Despite many efforts, the set of microbes inhabiting this environment is not fully known, limiting our ability to identify microbial content and to research it. In this work, we combine new microbial metagenomic assembled genomes from 51,052 samples, with previously published genomes to produce a curated set of 241,118 genomes. Based on this set, we procure a new and improved human gut microbiome reference set of 3594 high quality species genomes, which successfully matches 83.65% validation samples’ reads. This improved reference set contains 310 novel species, including one that exists in 19% of validation samples. Overall, this study provides a gut microbial genome reference set that can serve as a valuable resource for further research. Here, Leviatan et al. produce 241,118 genome assemblies to produce a new human gut microbiome reference set of 3,594 species genomes, of which 310 represent previously undescribed species, making the catalog a valuable resource for further research.
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Pereira J, Lupas AN. New β-Propellers Are Continuously Amplified From Single Blades in all Major Lineages of the β-Propeller Superfamily. Front Mol Biosci 2022; 9:895496. [PMID: 35755816 PMCID: PMC9218822 DOI: 10.3389/fmolb.2022.895496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 05/13/2022] [Indexed: 11/13/2022] Open
Abstract
β-Propellers are toroidal folds, in which consecutive supersecondary structure units of four anti-parallel β-strands-called blades-are arranged radially around a central axis. Uniquely among toroidal folds, blades span the full range of sequence symmetry, from near identity to complete divergence, indicating an ongoing process of amplification and differentiation. We have proposed that the major lineages of β-propellers arose through this mechanism and that therefore their last common ancestor was a single blade, not a fully formed β-propeller. Here we show that this process of amplification and differentiation is also widespread within individual lineages, yielding β-propellers with blades of more than 60% pairwise sequence identity in most major β-propeller families. In some cases, the blades are nearly identical, indicating a very recent amplification event, but even in cases where such recently amplified β-propellers have more than 80% overall sequence identity to each other, comparison of their DNA sequence shows that the amplification occurred independently.
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Affiliation(s)
- Joana Pereira
- Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany
| | - Andrei N Lupas
- Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany
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Samrot AV, Sean TC, Bhavya KS, Sahithya CS, Chan-drasekaran S, Palanisamy R, Robinson ER, Subbiah SK, Mok PL. Leptospiral Infection, Pathogenesis and Its Diagnosis-A Review. Pathogens 2021; 10:pathogens10020145. [PMID: 33535649 PMCID: PMC7912936 DOI: 10.3390/pathogens10020145] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/05/2020] [Accepted: 12/09/2020] [Indexed: 12/22/2022] Open
Abstract
Leptospirosis is a perplexing conundrum for many. In the existing literature, the pathophysiological mechanisms pertaining to leptospirosis is still not understood in full. Considered as a neglected tropical zoonotic disease, leptospirosis is culminating as a serious problem worldwide, seemingly existing as co-infections with various other unrelated diseases, including dengue and malaria. Misdiagnosis is also common as non-specific symptoms are documented extensively in the literature. This can easily lead to death, as the severe form of leptospirosis (Weil's disease) manifests as a complex of systemic complications, especially renal failure. The virulence of Leptospira sp. is usually attributed to the outer membrane proteins, including LipL32. With an armament of virulence factors at their disposal, their ability to easily adhere, invade and replicate within cells calls for a swift refinement in research progress to establish their exact pathophysiological framework. As an effort to reconstitute the current knowledge on leptospirosis, the basis of leptospiral infection, including its risk factors, classification, morphology, transmission, pathogenesis, co-infections and clinical manifestations are highlighted in this review. The various diagnostic techniques are also outlined with emphasis on their respective pros and cons.
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Affiliation(s)
- Antony V. Samrot
- School of Bioscience, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom, Selangor 42610, Malaysia;
- Correspondence: (A.V.S.); (P.L.M.)
| | - Tan Chuan Sean
- School of Bioscience, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom, Selangor 42610, Malaysia;
| | - Karanam Sai Bhavya
- Department of Biotechnology, School of Bio and Chemical Engineering, Sathyabama Institute of Science and Technology, Jeppiaar Nagar, Chennai, Tamil Nadu 627 011, India; (K.S.B.); (C.S.S.); (S.C.); (R.P.)
| | - Chamarthy Sai Sahithya
- Department of Biotechnology, School of Bio and Chemical Engineering, Sathyabama Institute of Science and Technology, Jeppiaar Nagar, Chennai, Tamil Nadu 627 011, India; (K.S.B.); (C.S.S.); (S.C.); (R.P.)
| | - SaiPriya Chan-drasekaran
- Department of Biotechnology, School of Bio and Chemical Engineering, Sathyabama Institute of Science and Technology, Jeppiaar Nagar, Chennai, Tamil Nadu 627 011, India; (K.S.B.); (C.S.S.); (S.C.); (R.P.)
| | - Raji Palanisamy
- Department of Biotechnology, School of Bio and Chemical Engineering, Sathyabama Institute of Science and Technology, Jeppiaar Nagar, Chennai, Tamil Nadu 627 011, India; (K.S.B.); (C.S.S.); (S.C.); (R.P.)
| | - Emilin Renitta Robinson
- Department of Food Processing Technology, Karunya Institute of Technology and Science, Coimbatore, Tamil Nadu 641 114, India;
| | - Suresh Kumar Subbiah
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia;
- Department of Biotechnology, Bharath Institute of Higher Education and Research (BIHER), Selaiyur, Tamil Nadu 600 073, India
- Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia
| | - Pooi Ling Mok
- Department of Biotechnology, Bharath Institute of Higher Education and Research (BIHER), Selaiyur, Tamil Nadu 600 073, India
- Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka P.O. Box 2014, Aljouf Province, Saudi Arabia
- Correspondence: (A.V.S.); (P.L.M.)
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Richardson JS, Videau LL, Williams CJ, Richardson DC. Broad Analysis of Vicinal Disulfides: Occurrences, Conformations with Cis or with Trans Peptides, and Functional Roles Including Sugar Binding. J Mol Biol 2017; 429:1321-1335. [PMID: 28336403 DOI: 10.1016/j.jmb.2017.03.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 03/12/2017] [Accepted: 03/13/2017] [Indexed: 10/19/2022]
Abstract
Vicinal disulfides between sequence-adjacent cysteine residues are very rare and rather startling structural features which play a variety of functional roles. Typically discussed as an isolated curiosity, they have never received a general treatment covering both cis and trans forms. Enabled by the growing database of high-resolution structures, required deposition of diffraction data, and improved methods for discriminating reliable from dubious cases, we identify and describe distinct protein families with reliably genuine examples of cis or trans vicinal disulfides and discuss their conformations, conservation, and functions. No cis-trans interconversions and only one case of catalytic redox function are seen. Some vicinal disulfides are essential to large, functionally coupled motions, whereas most form the centers of tightly packed internal regions. Their most widespread biological role is providing a rigid hydrophobic contact surface under the undecorated side of a sugar or multiring ligand, contributing an important aspect of binding specificity.
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Affiliation(s)
- Jane S Richardson
- Department of Biochemistry, 3711 Duke University Medical Center, Durham, NC 27710, USA.
| | - Lizbeth L Videau
- Department of Biochemistry, 3711 Duke University Medical Center, Durham, NC 27710, USA
| | | | - David C Richardson
- Department of Biochemistry, 3711 Duke University Medical Center, Durham, NC 27710, USA
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Xiang DF, Bigley AN, Ren Z, Xue H, Hull KG, Romo D, Raushel FM. Interrogation of the Substrate Profile and Catalytic Properties of the Phosphotriesterase from Sphingobium sp. Strain TCM1: An Enzyme Capable of Hydrolyzing Organophosphate Flame Retardants and Plasticizers. Biochemistry 2015; 54:7539-49. [DOI: 10.1021/acs.biochem.5b01144] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Dao Feng Xiang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Andrew N. Bigley
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Zhongjie Ren
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Haoran Xue
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Kenneth G. Hull
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Daniel Romo
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Frank M. Raushel
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
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Ptak CP, Hsieh CL, Lin YP, Maltsev AS, Raman R, Sharma Y, Oswald RE, Chang YF. NMR solution structure of the terminal immunoglobulin-like domain from the leptospira host-interacting outer membrane protein, LigB. Biochemistry 2014; 53:5249-60. [PMID: 25068811 PMCID: PMC4139157 DOI: 10.1021/bi500669u] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A number of surface proteins specific to pathogenic strains of Leptospira have been identified. The Lig protein family has shown promise as a marker in typing leptospiral isolates for pathogenesis and as an antigen in vaccines. We used NMR spectroscopy to solve the solution structure of the twelfth immunoglobulin-like (Ig-like) repeat domain from LigB (LigB-12). The fold is similar to that of other bacterial Ig-like domains and comprised mainly of β-strands that form a β-sandwich based on a Greek-key folding arrangement. Based on sequence analysis and conservation of structurally important residues, homology models for the other LigB Ig-like domains were generated. The set of LigB models illustrates the electrostatic differences between the domains as well as the possible interactions between neighboring domains. Understanding the structure of the extracellular portion of LigB and related proteins is important for developing diagnostic methods and new therapeutics directed toward leptospirosis.
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Affiliation(s)
- Christopher P Ptak
- Department of Population Medicine and Diagnostic Sciences and ‡Department of Molecular Medicine, College of Veterinary Medicine, Cornell University , Ithaca, New York 14853, United States
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Fraga TR, Chura-Chambi RM, Gonçales AP, Morais ZM, Vasconcellos SA, Morganti L, Martins EA. Refolding of the recombinant protein OmpA70 from Leptospira interrogans from inclusion bodies using high hydrostatic pressure and partial characterization of its immunological properties. J Biotechnol 2010; 148:156-62. [DOI: 10.1016/j.jbiotec.2010.04.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Revised: 02/04/2010] [Accepted: 04/21/2010] [Indexed: 10/19/2022]
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Schulze RJ, Chen S, Kumru OS, Zückert WR. Translocation of Borrelia burgdorferi surface lipoprotein OspA through the outer membrane requires an unfolded conformation and can initiate at the C-terminus. Mol Microbiol 2010; 76:1266-78. [PMID: 20398211 DOI: 10.1111/j.1365-2958.2010.07172.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Borrelia burgdorferi surface lipoproteins are essential to the pathogenesis of Lyme borreliosis, but the mechanisms responsible for their localization are only beginning to emerge. We have previously demonstrated the critical nature of the amino-terminal 'tether' domain of the mature lipoprotein for sorting a fluorescent reporter to the Borrelia cell surface. Here, we show that individual deletion of four contiguous residues within the tether of major surface lipoprotein OspA results in its inefficient translocation across the Borrelia outer membrane. Intriguingly, C-terminal epitope tags of these N-terminal deletion mutants were selectively surface-exposed. Fold-destabilizing C-terminal point mutations and deletions did not block OspA secretion, but rather restored one of the otherwise periplasmic tether mutants to the bacterial surface. Together, these data indicate that disturbance of a confined tether feature leads to premature folding of OspA in the periplasm and thereby prevents secretion through the outer membrane. Furthermore, they suggest that OspA emerges tail-first on the bacterial surface, yet independent of a specific C-terminal targeting peptide sequence.
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Affiliation(s)
- Ryan J Schulze
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Mail Stop 3029, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
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